Starting phenix.real_space_refine on Thu Jul 2 05:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy6_33512/07_2026/7xy6_33512.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4481 2.51 5 N 1229 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7044 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1851 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2212 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'I5D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7044 At special positions: 0 Unit cell: (85.44, 101.76, 133.44, 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 48 16.00 O 1286 8.00 N 1229 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 357.6 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 46.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.795A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.556A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 230 " --> pdb=" O TRP A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.533A pdb=" N ASN A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.547A pdb=" N LEU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.581A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.511A pdb=" N ILE A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 removed outlier: 3.870A pdb=" N ILE A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.932A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.757A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.712A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.683A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 34 Processing helix chain 'R' and resid 40 through 70 removed outlier: 4.180A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 4.117A pdb=" N GLY R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.700A pdb=" N CYS R 78 " --> pdb=" O ASP R 74 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA R 82 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR R 89 " --> pdb=" O VAL R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 178 through 185 Processing helix chain 'R' and resid 185 through 191 Processing helix chain 'R' and resid 191 through 218 removed outlier: 3.608A pdb=" N LEU R 218 " --> pdb=" O GLN R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 4.169A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Proline residue: R 249 - end of helix removed outlier: 3.600A pdb=" N VAL R 253 " --> pdb=" O PRO R 249 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS R 255 " --> pdb=" O HIS R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 266 removed outlier: 3.976A pdb=" N ASN R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 291 removed outlier: 4.254A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN R 286 " --> pdb=" O ASN R 282 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 207 removed outlier: 3.521A pdb=" N PHE A 205 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 34 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 236 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 237 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE A 273 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 239 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN A 275 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.018A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.802A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.864A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.605A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.961A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.666A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 73 340 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1146 1.26 - 1.40: 1821 1.40 - 1.54: 4141 1.54 - 1.68: 12 1.68 - 1.82: 67 Bond restraints: 7187 Sorted by residual: bond pdb=" C16 I5D R 501 " pdb=" C17 I5D R 501 " ideal model delta sigma weight residual 1.386 1.525 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C4' I5D R 501 " pdb=" C5' I5D R 501 " ideal model delta sigma weight residual 1.396 1.529 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C8 I5D R 501 " pdb=" NAA I5D R 501 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C6 I5D R 501 " pdb=" N1 I5D R 501 " ideal model delta sigma weight residual 1.337 1.460 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C10 I5D R 501 " pdb=" C11 I5D R 501 " ideal model delta sigma weight residual 1.399 1.521 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 7182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 9616 1.83 - 3.67: 105 3.67 - 5.50: 20 5.50 - 7.33: 5 7.33 - 9.16: 1 Bond angle restraints: 9747 Sorted by residual: angle pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" CD PRO A 296 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 angle pdb=" N LEU A 376 " pdb=" CA LEU A 376 " pdb=" C LEU A 376 " ideal model delta sigma weight residual 114.04 109.95 4.09 1.24e+00 6.50e-01 1.09e+01 angle pdb=" C1' I5D R 501 " pdb=" S1 I5D R 501 " pdb=" C5 I5D R 501 " ideal model delta sigma weight residual 101.05 110.21 -9.16 3.00e+00 1.11e-01 9.33e+00 angle pdb=" CA SER R 279 " pdb=" C SER R 279 " pdb=" O SER R 279 " ideal model delta sigma weight residual 120.55 117.94 2.61 1.06e+00 8.90e-01 6.06e+00 angle pdb=" CB MET G 38 " pdb=" CG MET G 38 " pdb=" SD MET G 38 " ideal model delta sigma weight residual 112.70 120.03 -7.33 3.00e+00 1.11e-01 5.96e+00 ... (remaining 9742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 3892 21.67 - 43.34: 330 43.34 - 65.00: 38 65.00 - 86.67: 14 86.67 - 108.34: 3 Dihedral angle restraints: 4277 sinusoidal: 1666 harmonic: 2611 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 171 " pdb=" CB CYS R 171 " ideal model delta sinusoidal sigma weight residual 93.00 159.70 -66.70 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" C1' I5D R 501 " pdb=" C5 I5D R 501 " pdb=" S1 I5D R 501 " pdb=" C6 I5D R 501 " ideal model delta sinusoidal sigma weight residual -178.49 -70.15 -108.34 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O6 I5D R 501 " pdb=" C5 I5D R 501 " pdb=" C6 I5D R 501 " pdb=" S1 I5D R 501 " ideal model delta sinusoidal sigma weight residual -1.83 100.11 -101.94 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 4274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 951 0.058 - 0.117: 152 0.117 - 0.175: 9 0.175 - 0.233: 0 0.233 - 0.291: 1 Chirality restraints: 1113 Sorted by residual: chirality pdb=" C13 I5D R 501 " pdb=" C12 I5D R 501 " pdb=" C14 I5D R 501 " pdb=" C15 I5D R 501 " both_signs ideal model delta sigma weight residual True 2.41 2.71 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1110 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 I5D R 501 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C6 I5D R 501 " -0.093 2.00e-02 2.50e+03 pdb=" N1 I5D R 501 " 0.030 2.00e-02 2.50e+03 pdb=" O6 I5D R 501 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 295 " 0.042 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 296 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO G 49 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.028 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1064 2.76 - 3.29: 6367 3.29 - 3.83: 11131 3.83 - 4.36: 12015 4.36 - 4.90: 21948 Nonbonded interactions: 52525 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP B 254 " pdb=" N LEU B 255 " model vdw 2.248 3.120 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.270 3.040 nonbonded pdb=" O ILE G 25 " pdb=" NH1 ARG G 27 " model vdw 2.278 3.120 nonbonded pdb=" OG SER R 21 " pdb=" OG SER R 283 " model vdw 2.284 3.040 ... (remaining 52520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.005 0.139 7188 Z= 0.265 Angle : 0.542 9.164 9749 Z= 0.296 Chirality : 0.041 0.291 1113 Planarity : 0.004 0.061 1240 Dihedral : 15.963 108.338 2580 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.13 % Allowed : 18.33 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.29), residues: 881 helix: 2.00 (0.28), residues: 370 sheet: 0.51 (0.40), residues: 162 loop : -0.86 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 368 TYR 0.012 0.001 TYR R 299 PHE 0.010 0.001 PHE R 84 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.26 ( 7187) covalent geometry : angle 0.54236 / 0.30 ( 9747) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.69561 / 0.32 ( 2) hydrogen bonds : bond 0.17968 / 12.56 ( 340) hydrogen bonds : angle 6.18149 / 4.34 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 206 GLN cc_start: 0.8485 (pt0) cc_final: 0.8273 (pt0) REVERT: B 214 ARG cc_start: 0.8102 (ptp-110) cc_final: 0.7874 (ptp-110) REVERT: R 175 ASN cc_start: 0.8527 (m110) cc_final: 0.8321 (m110) REVERT: R 245 LEU cc_start: 0.8290 (tp) cc_final: 0.8078 (tt) outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.5642 time to fit residues: 91.9382 Evaluate side-chains 155 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 259 GLN R 25 ASN R 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118613 restraints weight = 10366.843| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.52 r_work: 0.3424 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7188 Z= 0.137 Angle : 0.499 9.381 9749 Z= 0.267 Chirality : 0.041 0.128 1113 Planarity : 0.004 0.048 1240 Dihedral : 6.912 95.895 987 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.19 % Allowed : 15.67 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 881 helix: 2.09 (0.27), residues: 391 sheet: 0.52 (0.40), residues: 159 loop : -1.00 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.009 0.001 TYR A 322 PHE 0.012 0.001 PHE R 80 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7187) covalent geometry : angle 0.49891 / 0.27 ( 9747) SS BOND : bond 0.00228 / 0.12 ( 1) SS BOND : angle 0.83295 / 0.46 ( 2) hydrogen bonds : bond 0.06091 / 4.20 ( 340) hydrogen bonds : angle 4.42758 / 3.03 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8185 (ptp-110) REVERT: B 298 ASP cc_start: 0.7972 (t0) cc_final: 0.7699 (t70) REVERT: R 212 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7671 (mm110) REVERT: R 245 LEU cc_start: 0.8224 (tp) cc_final: 0.7985 (tt) REVERT: R 274 MET cc_start: 0.6716 (mmt) cc_final: 0.6354 (mmt) outliers start: 24 outliers final: 10 residues processed: 171 average time/residue: 0.5217 time to fit residues: 93.7444 Evaluate side-chains 163 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 overall best weight: 0.3090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119692 restraints weight = 10276.318| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.60 r_work: 0.3441 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7188 Z= 0.105 Angle : 0.477 8.424 9749 Z= 0.250 Chirality : 0.040 0.130 1113 Planarity : 0.004 0.043 1240 Dihedral : 6.653 98.004 987 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.79 % Allowed : 18.19 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.29), residues: 881 helix: 2.26 (0.27), residues: 397 sheet: 0.48 (0.41), residues: 163 loop : -1.01 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.008 0.001 TYR A 322 PHE 0.012 0.001 PHE R 80 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.000 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 7187) covalent geometry : angle 0.47697 / 0.25 ( 9747) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 0.88428 / 0.50 ( 2) hydrogen bonds : bond 0.04838 / 3.35 ( 340) hydrogen bonds : angle 4.13800 / 2.82 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7921 (ptp-110) cc_final: 0.7684 (ptp-110) REVERT: B 20 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: B 150 ARG cc_start: 0.8528 (mpt180) cc_final: 0.8200 (mmt-90) REVERT: B 188 MET cc_start: 0.7783 (mmm) cc_final: 0.7579 (mmm) REVERT: B 214 ARG cc_start: 0.8467 (ptp-110) cc_final: 0.8182 (ptp-110) REVERT: B 298 ASP cc_start: 0.7976 (t0) cc_final: 0.7583 (t70) REVERT: R 212 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7635 (mm110) REVERT: R 245 LEU cc_start: 0.8248 (tp) cc_final: 0.8020 (tt) REVERT: R 274 MET cc_start: 0.6738 (mmt) cc_final: 0.6399 (mmt) outliers start: 21 outliers final: 8 residues processed: 176 average time/residue: 0.4696 time to fit residues: 87.0857 Evaluate side-chains 163 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 0.1980 chunk 47 optimal weight: 0.0010 chunk 63 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN B 239 ASN B 340 ASN R 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119125 restraints weight = 10393.241| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.58 r_work: 0.3433 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7188 Z= 0.111 Angle : 0.475 8.648 9749 Z= 0.250 Chirality : 0.040 0.129 1113 Planarity : 0.004 0.043 1240 Dihedral : 6.405 96.814 987 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.92 % Allowed : 17.80 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.29), residues: 881 helix: 2.27 (0.27), residues: 395 sheet: 0.47 (0.41), residues: 163 loop : -0.97 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.009 0.001 TYR A 322 PHE 0.012 0.001 PHE R 187 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7187) covalent geometry : angle 0.47470 / 0.25 ( 9747) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 0.80895 / 0.47 ( 2) hydrogen bonds : bond 0.04870 / 3.35 ( 340) hydrogen bonds : angle 4.04829 / 2.76 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8127 (tttp) cc_final: 0.7922 (tttm) REVERT: A 263 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7713 (ptp-110) REVERT: B 20 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7382 (p0) REVERT: B 188 MET cc_start: 0.7793 (mmm) cc_final: 0.7540 (mmm) REVERT: B 214 ARG cc_start: 0.8513 (ptp-110) cc_final: 0.8230 (ptp-110) REVERT: B 298 ASP cc_start: 0.8021 (t0) cc_final: 0.7588 (t70) REVERT: R 245 LEU cc_start: 0.8263 (tp) cc_final: 0.8045 (tt) outliers start: 22 outliers final: 10 residues processed: 168 average time/residue: 0.4607 time to fit residues: 81.5972 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 214 GLN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN B 239 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117680 restraints weight = 10282.514| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.48 r_work: 0.3406 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7188 Z= 0.160 Angle : 0.518 9.033 9749 Z= 0.272 Chirality : 0.042 0.132 1113 Planarity : 0.004 0.045 1240 Dihedral : 6.318 95.538 987 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.92 % Allowed : 17.66 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 881 helix: 2.12 (0.27), residues: 395 sheet: 0.50 (0.41), residues: 161 loop : -1.02 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 215 TYR 0.009 0.001 TYR B 145 PHE 0.014 0.002 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7187) covalent geometry : angle 0.51762 / 0.27 ( 9747) SS BOND : bond 0.00248 / 0.13 ( 1) SS BOND : angle 0.96100 / 0.56 ( 2) hydrogen bonds : bond 0.05907 / 4.05 ( 340) hydrogen bonds : angle 4.16655 / 2.84 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8469 (ttmm) REVERT: A 263 ARG cc_start: 0.7967 (ptp-110) cc_final: 0.7719 (ptp-110) REVERT: B 20 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7426 (p0) REVERT: B 214 ARG cc_start: 0.8493 (ptp-110) cc_final: 0.8223 (ptp-110) REVERT: B 298 ASP cc_start: 0.8041 (t0) cc_final: 0.7652 (t70) REVERT: G 18 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8414 (tm-30) REVERT: R 25 ASN cc_start: 0.8155 (m-40) cc_final: 0.7802 (m-40) REVERT: R 176 VAL cc_start: 0.7324 (t) cc_final: 0.7054 (m) REVERT: R 245 LEU cc_start: 0.8288 (tp) cc_final: 0.8056 (tt) outliers start: 22 outliers final: 12 residues processed: 175 average time/residue: 0.4639 time to fit residues: 85.6057 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 285 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN B 239 ASN R 145 ASN R 186 ASN R 273 ASN R 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116987 restraints weight = 10356.467| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.51 r_work: 0.3395 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7188 Z= 0.152 Angle : 0.528 9.875 9749 Z= 0.273 Chirality : 0.041 0.131 1113 Planarity : 0.004 0.045 1240 Dihedral : 6.229 94.118 987 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 17.93 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.29), residues: 881 helix: 2.20 (0.27), residues: 393 sheet: 0.56 (0.41), residues: 161 loop : -0.94 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.011 0.001 TYR A 246 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7187) covalent geometry : angle 0.52813 / 0.27 ( 9747) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 0.94082 / 0.54 ( 2) hydrogen bonds : bond 0.05936 / 4.06 ( 340) hydrogen bonds : angle 4.14645 / 2.83 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8473 (ttmm) REVERT: A 263 ARG cc_start: 0.7854 (ptp-110) cc_final: 0.7584 (ptp-110) REVERT: B 20 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7484 (p0) REVERT: B 214 ARG cc_start: 0.8480 (ptp-110) cc_final: 0.8192 (ptp-110) REVERT: B 255 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7228 (mp) REVERT: B 258 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7599 (t70) REVERT: B 298 ASP cc_start: 0.8031 (t0) cc_final: 0.7634 (t70) REVERT: G 18 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8380 (tm-30) REVERT: R 25 ASN cc_start: 0.8120 (m-40) cc_final: 0.7788 (m-40) REVERT: R 176 VAL cc_start: 0.7286 (t) cc_final: 0.7014 (m) REVERT: R 245 LEU cc_start: 0.8254 (tp) cc_final: 0.8025 (tt) outliers start: 26 outliers final: 12 residues processed: 178 average time/residue: 0.4511 time to fit residues: 84.7441 Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN B 239 ASN R 145 ASN R 186 ASN R 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117187 restraints weight = 10223.048| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.53 r_work: 0.3410 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7188 Z= 0.129 Angle : 0.513 8.804 9749 Z= 0.264 Chirality : 0.041 0.127 1113 Planarity : 0.004 0.044 1240 Dihedral : 5.994 91.413 987 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.52 % Allowed : 20.05 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 881 helix: 2.27 (0.27), residues: 393 sheet: 0.56 (0.42), residues: 161 loop : -0.92 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 368 TYR 0.009 0.001 TYR A 246 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7187) covalent geometry : angle 0.51284 / 0.26 ( 9747) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.86741 / 0.50 ( 2) hydrogen bonds : bond 0.05436 / 3.72 ( 340) hydrogen bonds : angle 4.06540 / 2.77 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8470 (ttmm) REVERT: A 263 ARG cc_start: 0.7823 (ptp-110) cc_final: 0.7548 (ptp-110) REVERT: B 20 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7457 (p0) REVERT: B 258 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (t70) REVERT: B 298 ASP cc_start: 0.8033 (t0) cc_final: 0.7634 (t70) REVERT: G 18 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8299 (tm-30) REVERT: R 25 ASN cc_start: 0.8096 (m-40) cc_final: 0.7730 (m-40) REVERT: R 176 VAL cc_start: 0.7238 (t) cc_final: 0.6943 (m) REVERT: R 245 LEU cc_start: 0.8239 (tp) cc_final: 0.8005 (tt) outliers start: 19 outliers final: 10 residues processed: 173 average time/residue: 0.4632 time to fit residues: 84.5361 Evaluate side-chains 173 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN B 239 ASN R 43 ASN R 145 ASN R 282 ASN R 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118153 restraints weight = 10320.316| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.47 r_work: 0.3415 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7188 Z= 0.126 Angle : 0.505 8.769 9749 Z= 0.262 Chirality : 0.041 0.127 1113 Planarity : 0.004 0.044 1240 Dihedral : 5.701 87.252 987 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.92 % Allowed : 19.65 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 881 helix: 2.28 (0.27), residues: 393 sheet: 0.54 (0.42), residues: 156 loop : -0.93 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.009 0.001 TYR A 322 PHE 0.012 0.001 PHE B 241 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7187) covalent geometry : angle 0.50492 / 0.26 ( 9747) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.84677 / 0.49 ( 2) hydrogen bonds : bond 0.05314 / 3.64 ( 340) hydrogen bonds : angle 4.03377 / 2.75 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8505 (ttmm) REVERT: A 263 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7565 (ptp-110) REVERT: B 20 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7489 (p0) REVERT: B 188 MET cc_start: 0.7813 (mmm) cc_final: 0.7517 (mmm) REVERT: B 258 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7565 (t70) REVERT: B 298 ASP cc_start: 0.8016 (t0) cc_final: 0.7652 (t70) REVERT: B 304 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7612 (ttm170) REVERT: G 18 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8300 (tm-30) REVERT: R 176 VAL cc_start: 0.7247 (t) cc_final: 0.6955 (m) REVERT: R 245 LEU cc_start: 0.8283 (tp) cc_final: 0.8047 (tt) outliers start: 22 outliers final: 15 residues processed: 166 average time/residue: 0.4417 time to fit residues: 77.4297 Evaluate side-chains 170 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 0.0050 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117504 restraints weight = 10265.277| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.51 r_work: 0.3411 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7188 Z= 0.131 Angle : 0.507 8.825 9749 Z= 0.264 Chirality : 0.041 0.127 1113 Planarity : 0.004 0.044 1240 Dihedral : 5.456 81.867 987 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.92 % Allowed : 19.52 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 881 helix: 2.30 (0.27), residues: 393 sheet: 0.54 (0.42), residues: 156 loop : -0.94 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.009 0.001 TYR A 322 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7187) covalent geometry : angle 0.50723 / 0.26 ( 9747) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.84986 / 0.49 ( 2) hydrogen bonds : bond 0.05418 / 3.71 ( 340) hydrogen bonds : angle 4.03541 / 2.75 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8518 (ttmm) REVERT: A 263 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7576 (ptp-110) REVERT: B 20 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 150 ARG cc_start: 0.8604 (mpt180) cc_final: 0.8367 (mmt-90) REVERT: B 188 MET cc_start: 0.7871 (mmm) cc_final: 0.7593 (mmm) REVERT: B 258 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7576 (t70) REVERT: B 298 ASP cc_start: 0.8025 (t0) cc_final: 0.7664 (t70) REVERT: G 18 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8305 (tm-30) REVERT: R 176 VAL cc_start: 0.7257 (t) cc_final: 0.6964 (m) REVERT: R 195 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6809 (tt) REVERT: R 245 LEU cc_start: 0.8279 (tp) cc_final: 0.8058 (tt) outliers start: 22 outliers final: 14 residues processed: 166 average time/residue: 0.4427 time to fit residues: 77.4272 Evaluate side-chains 171 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117048 restraints weight = 10201.886| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.49 r_work: 0.3402 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7188 Z= 0.144 Angle : 0.522 8.947 9749 Z= 0.272 Chirality : 0.041 0.128 1113 Planarity : 0.004 0.044 1240 Dihedral : 5.267 76.710 987 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.39 % Allowed : 20.32 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.29), residues: 881 helix: 2.26 (0.27), residues: 393 sheet: 0.57 (0.42), residues: 156 loop : -0.93 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.010 0.001 TYR A 246 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7187) covalent geometry : angle 0.52170 / 0.27 ( 9747) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 0.92508 / 0.53 ( 2) hydrogen bonds : bond 0.05787 / 3.96 ( 340) hydrogen bonds : angle 4.09556 / 2.79 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8518 (ttmm) REVERT: A 263 ARG cc_start: 0.7884 (ptp-110) cc_final: 0.7621 (ptp-110) REVERT: B 20 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7493 (p0) REVERT: B 150 ARG cc_start: 0.8607 (mpt180) cc_final: 0.8350 (mmt-90) REVERT: B 188 MET cc_start: 0.7879 (mmm) cc_final: 0.7571 (mmm) REVERT: B 258 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7590 (t70) REVERT: B 298 ASP cc_start: 0.8031 (t0) cc_final: 0.7688 (t70) REVERT: G 18 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8312 (tm-30) REVERT: R 25 ASN cc_start: 0.8101 (m-40) cc_final: 0.7756 (m-40) REVERT: R 176 VAL cc_start: 0.7297 (t) cc_final: 0.7016 (m) REVERT: R 195 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6834 (tt) REVERT: R 245 LEU cc_start: 0.8249 (tp) cc_final: 0.8030 (tt) outliers start: 18 outliers final: 14 residues processed: 174 average time/residue: 0.4478 time to fit residues: 82.0843 Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 CYS Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 6 optimal weight: 0.0570 chunk 81 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN R 145 ASN R 186 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117898 restraints weight = 10178.308| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.53 r_work: 0.3417 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7188 Z= 0.122 Angle : 0.505 8.779 9749 Z= 0.263 Chirality : 0.041 0.126 1113 Planarity : 0.004 0.043 1240 Dihedral : 5.212 80.248 987 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.12 % Allowed : 20.72 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 881 helix: 2.33 (0.27), residues: 393 sheet: 0.60 (0.42), residues: 156 loop : -0.94 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.010 0.001 TYR A 322 PHE 0.013 0.001 PHE R 80 TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7187) covalent geometry : angle 0.50440 / 0.26 ( 9747) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.87541 / 0.51 ( 2) hydrogen bonds : bond 0.05146 / 3.53 ( 340) hydrogen bonds : angle 3.99659 / 2.72 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.42 seconds wall clock time: 38 minutes 27.48 seconds (2307.48 seconds total)