Starting phenix.real_space_refine on Fri Sep 11 10:11:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kpf_0744/09_2026/6kpf_0744.cif" } resolution = 2.9 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= 0.000 sd= 0.005 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 66 5.16 5 C 5599 2.51 5 N 1493 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1708 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'E3R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8775 At special positions: 0 Unit cell: (118.56, 100.88, 120.64, 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 66 16.00 O 1617 8.00 N 1493 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.61 Conformation dependent library (CDL) restraints added in 340.6 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 34.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.514A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.505A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.919A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.936A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.757A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.543A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.724A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.717A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 30 through 61 removed outlier: 4.424A pdb=" N LEU R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 66 removed outlier: 3.602A pdb=" N ARG R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 86 Processing helix chain 'R' and resid 86 through 96 removed outlier: 3.638A pdb=" N VAL R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE R 94 " --> pdb=" O SER R 90 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 96 " --> pdb=" O VAL R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 131 removed outlier: 3.840A pdb=" N THR R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.522A pdb=" N THR R 153 " --> pdb=" O ARG R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 216 removed outlier: 3.811A pdb=" N SER R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 224 Processing helix chain 'R' and resid 238 through 245 Processing helix chain 'R' and resid 245 through 254 removed outlier: 3.608A pdb=" N LEU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 263 Processing helix chain 'R' and resid 265 through 269 removed outlier: 3.946A pdb=" N SER R 268 " --> pdb=" O MET R 265 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 269 " --> pdb=" O ALA R 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 269' Processing helix chain 'R' and resid 279 through 285 Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 294 through 300 Processing helix chain 'R' and resid 303 through 311 removed outlier: 3.586A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER R 309 " --> pdb=" O GLU R 305 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.525A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.718A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.918A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.083A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.374A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.659A 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: 3.668A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.558A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.739A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.213A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.579A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148 393 hydrogen bonds defined for protein. 1098 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: 1.33 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1401 1.29 - 1.43: 2404 1.43 - 1.57: 5061 1.57 - 1.70: 1 1.70 - 1.84: 95 Bond restraints: 8962 Sorted by residual: bond pdb=" CA ILE R 186 " pdb=" CB ILE R 186 " ideal model delta sigma weight residual 1.537 1.565 -0.028 1.29e-02 6.01e+03 4.74e+00 bond pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.22e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.17e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.40e+00 bond pdb=" C4 E3R R 401 " pdb=" C5 E3R R 401 " ideal model delta sigma weight residual 1.399 1.435 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11906 2.64 - 5.29: 196 5.29 - 7.93: 33 7.93 - 10.58: 11 10.58 - 13.22: 3 Bond angle restraints: 12149 Sorted by residual: angle pdb=" CA CYS R 179 " pdb=" CB CYS R 179 " pdb=" SG CYS R 179 " ideal model delta sigma weight residual 114.40 126.55 -12.15 2.30e+00 1.89e-01 2.79e+01 angle pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C7 E3R R 401 " ideal model delta sigma weight residual 111.05 124.27 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta sigma weight residual 122.03 113.59 8.44 2.01e+00 2.48e-01 1.76e+01 angle pdb=" C3 E3R R 401 " pdb=" C4 E3R R 401 " pdb=" O3 E3R R 401 " ideal model delta sigma weight residual 120.37 108.10 12.27 3.00e+00 1.11e-01 1.67e+01 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 4741 18.06 - 36.12: 463 36.12 - 54.18: 84 54.18 - 72.24: 12 72.24 - 90.30: 9 Dihedral angle restraints: 5309 sinusoidal: 2025 harmonic: 3284 Sorted by residual: dihedral pdb=" CA PRO R 178 " pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta harmonic sigma weight residual 180.00 124.09 55.91 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 5306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1126 0.063 - 0.126: 229 0.126 - 0.189: 27 0.189 - 0.252: 6 0.252 - 0.315: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C12 E3R R 401 " pdb=" C14 E3R R 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.89 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C8 E3R R 401 " pdb=" C13 E3R R 401 " pdb=" C7 E3R R 401 " pdb=" C9 E3R R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.73 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1387 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO R 168 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 259 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 260 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 186 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO R 187 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.036 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1268 2.75 - 3.29: 7769 3.29 - 3.83: 15111 3.83 - 4.36: 18525 4.36 - 4.90: 31676 Nonbonded interactions: 74349 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ARG B 129 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.258 3.040 ... (remaining 74344 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.490 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: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.007 0.080 8965 Z= 0.298 Angle : 0.909 13.222 12155 Z= 0.468 Chirality : 0.054 0.315 1390 Planarity : 0.007 0.091 1521 Dihedral : 14.927 90.302 3182 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.46 (0.20), residues: 1117 helix: -4.64 (0.09), residues: 384 sheet: -1.43 (0.28), residues: 285 loop : -2.14 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 179 TYR 0.032 0.002 TYR S 178 PHE 0.020 0.002 PHE S 27 TRP 0.016 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.30 ( 8962) covalent geometry : angle 0.90873 / 0.47 (12149) SS BOND : bond 0.01118 / 0.58 ( 3) SS BOND : angle 1.53984 / 0.88 ( 6) hydrogen bonds : bond 0.27140 / 17.32 ( 386) hydrogen bonds : angle 10.35930 / 7.07 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.337 Fit side-chains REVERT: A 35 LYS cc_start: 0.8564 (mttp) cc_final: 0.8236 (mtmt) REVERT: B 325 MET cc_start: 0.8453 (tpp) cc_final: 0.8207 (tpp) REVERT: C 20 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8273 (mtmm) REVERT: C 47 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 53 PRO cc_start: 0.7155 (Cg_exo) cc_final: 0.6937 (Cg_endo) REVERT: R 33 LYS cc_start: 0.4799 (ptpt) cc_final: 0.4578 (pttm) REVERT: R 115 MET cc_start: 0.7393 (ttp) cc_final: 0.7078 (ttm) REVERT: R 147 ARG cc_start: 0.6376 (ttt-90) cc_final: 0.5990 (ttt180) REVERT: R 157 MET cc_start: 0.6415 (tpp) cc_final: 0.6183 (tpp) REVERT: R 245 LYS cc_start: 0.6932 (mmpt) cc_final: 0.6726 (mmpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.6079 time to fit residues: 102.2754 Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 244 HIS A 322 HIS B 32 GLN B 62 HIS B 119 ASN B 175 GLN B 340 ASN C 18 GLN R 217 HIS R 295 ASN S 3 GLN S 182 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.160062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104955 restraints weight = 10119.132| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.19 r_work: 0.2923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8965 Z= 0.200 Angle : 0.634 10.743 12155 Z= 0.335 Chirality : 0.044 0.167 1390 Planarity : 0.006 0.073 1521 Dihedral : 5.959 58.043 1240 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 3.19 % Allowed : 17.55 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.22), residues: 1117 helix: -2.57 (0.20), residues: 379 sheet: -1.10 (0.28), residues: 281 loop : -1.65 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.024 0.002 TYR S 178 PHE 0.015 0.002 PHE A 189 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 8962) covalent geometry : angle 0.63292 / 0.33 (12149) SS BOND : bond 0.00669 / 0.34 ( 3) SS BOND : angle 1.99670 / 1.16 ( 6) hydrogen bonds : bond 0.04764 / 3.10 ( 386) hydrogen bonds : angle 5.58577 / 3.85 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8676 (ttp) cc_final: 0.8308 (mtp) REVERT: A 32 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7384 (mtm110) REVERT: A 35 LYS cc_start: 0.8830 (mttp) cc_final: 0.8228 (mtmt) REVERT: A 198 MET cc_start: 0.8740 (mtm) cc_final: 0.8428 (ttp) REVERT: B 23 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7755 (tptt) REVERT: B 325 MET cc_start: 0.9086 (tpp) cc_final: 0.8858 (tpp) REVERT: C 46 LYS cc_start: 0.8563 (mmtm) cc_final: 0.7870 (mmtt) REVERT: C 47 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 53 PRO cc_start: 0.7183 (Cg_exo) cc_final: 0.6982 (Cg_endo) REVERT: R 71 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7275 (mm) REVERT: R 157 MET cc_start: 0.5764 (tpp) cc_final: 0.5523 (tpp) REVERT: R 286 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.5060 (mmp) outliers start: 30 outliers final: 9 residues processed: 155 average time/residue: 0.6139 time to fit residues: 100.7291 Evaluate side-chains 137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS S 3 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.160254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106336 restraints weight = 9965.353| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.12 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8965 Z= 0.152 Angle : 0.587 10.790 12155 Z= 0.305 Chirality : 0.042 0.165 1390 Planarity : 0.005 0.066 1521 Dihedral : 5.661 59.874 1240 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.62 % Allowed : 19.68 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.23), residues: 1117 helix: -1.41 (0.25), residues: 382 sheet: -1.10 (0.28), residues: 278 loop : -1.35 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 190 TYR 0.020 0.001 TYR S 178 PHE 0.014 0.001 PHE S 27 TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8962) covalent geometry : angle 0.58571 / 0.30 (12149) SS BOND : bond 0.00691 / 0.35 ( 3) SS BOND : angle 1.85227 / 1.07 ( 6) hydrogen bonds : bond 0.04051 / 2.62 ( 386) hydrogen bonds : angle 5.09150 / 3.52 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8647 (ttp) cc_final: 0.8309 (mtp) REVERT: A 35 LYS cc_start: 0.8829 (mttp) cc_final: 0.8236 (mtmt) REVERT: A 198 MET cc_start: 0.8691 (mtm) cc_final: 0.8393 (ttp) REVERT: A 229 ASP cc_start: 0.6779 (p0) cc_final: 0.6564 (p0) REVERT: B 23 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7744 (tptt) REVERT: B 161 SER cc_start: 0.9495 (p) cc_final: 0.9268 (p) REVERT: B 234 PHE cc_start: 0.9509 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: B 300 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 47 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 53 PRO cc_start: 0.7176 (Cg_exo) cc_final: 0.6944 (Cg_endo) REVERT: R 71 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7105 (mm) REVERT: R 115 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6176 (tmm) REVERT: R 245 LYS cc_start: 0.6582 (mmpt) cc_final: 0.6335 (mmpt) REVERT: R 286 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4921 (mtp) REVERT: R 293 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7102 (ptt) outliers start: 34 outliers final: 16 residues processed: 156 average time/residue: 0.5656 time to fit residues: 93.8322 Evaluate side-chains 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107793 restraints weight = 10187.767| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.21 r_work: 0.3124 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8965 Z= 0.123 Angle : 0.558 11.013 12155 Z= 0.287 Chirality : 0.042 0.159 1390 Planarity : 0.004 0.062 1521 Dihedral : 5.414 56.036 1240 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.62 % Allowed : 20.64 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.62 (0.24), residues: 1117 helix: -0.75 (0.26), residues: 382 sheet: -0.99 (0.28), residues: 274 loop : -1.22 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 190 TYR 0.016 0.001 TYR S 178 PHE 0.013 0.001 PHE S 27 TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8962) covalent geometry : angle 0.55656 / 0.29 (12149) SS BOND : bond 0.00676 / 0.35 ( 3) SS BOND : angle 1.79639 / 1.03 ( 6) hydrogen bonds : bond 0.03649 / 2.37 ( 386) hydrogen bonds : angle 4.80727 / 3.31 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: A 35 LYS cc_start: 0.8789 (mttp) cc_final: 0.8220 (mtmt) REVERT: A 198 MET cc_start: 0.8720 (mtm) cc_final: 0.8421 (ttp) REVERT: A 243 MET cc_start: 0.7345 (ttm) cc_final: 0.6800 (mtm) REVERT: B 23 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7708 (tptt) REVERT: B 161 SER cc_start: 0.9501 (p) cc_final: 0.9243 (p) REVERT: B 234 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.8960 (m-80) REVERT: B 300 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8650 (mt) REVERT: C 47 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8141 (mt-10) REVERT: C 53 PRO cc_start: 0.7110 (Cg_exo) cc_final: 0.6871 (Cg_endo) REVERT: R 115 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6099 (tmm) REVERT: R 157 MET cc_start: 0.5515 (tpp) cc_final: 0.5308 (tpp) REVERT: R 245 LYS cc_start: 0.6543 (mmpt) cc_final: 0.6305 (mmpt) REVERT: S 93 MET cc_start: 0.8832 (ttt) cc_final: 0.8624 (ttp) REVERT: S 137 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7879 (m) outliers start: 34 outliers final: 14 residues processed: 168 average time/residue: 0.5719 time to fit residues: 102.3873 Evaluate side-chains 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 295 ASN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105793 restraints weight = 10040.741| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.12 r_work: 0.2943 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8965 Z= 0.177 Angle : 0.592 11.226 12155 Z= 0.302 Chirality : 0.043 0.194 1390 Planarity : 0.004 0.055 1521 Dihedral : 5.525 57.216 1240 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.40 % Favored : 96.42 % Rotamer: Outliers : 4.47 % Allowed : 21.06 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.28 (0.25), residues: 1117 helix: -0.39 (0.27), residues: 380 sheet: -0.96 (0.28), residues: 280 loop : -0.99 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.022 0.002 TYR S 178 PHE 0.015 0.001 PHE S 27 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 8962) covalent geometry : angle 0.58977 / 0.30 (12149) SS BOND : bond 0.00604 / 0.31 ( 3) SS BOND : angle 2.61480 / 1.51 ( 6) hydrogen bonds : bond 0.03737 / 2.41 ( 386) hydrogen bonds : angle 4.78418 / 3.30 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8410 (mtp) REVERT: A 35 LYS cc_start: 0.8838 (mttp) cc_final: 0.8292 (mtmt) REVERT: A 198 MET cc_start: 0.8739 (mtm) cc_final: 0.8519 (ttp) REVERT: A 261 ASP cc_start: 0.8343 (p0) cc_final: 0.7982 (p0) REVERT: A 273 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7941 (tt) REVERT: B 23 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7749 (tptt) REVERT: B 46 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7661 (mtp-110) REVERT: B 161 SER cc_start: 0.9491 (p) cc_final: 0.9230 (p) REVERT: B 234 PHE cc_start: 0.9526 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: C 47 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8188 (mt-10) REVERT: R 115 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6192 (tmm) REVERT: R 157 MET cc_start: 0.5620 (tpp) cc_final: 0.5408 (tpp) REVERT: R 245 LYS cc_start: 0.6593 (mmpt) cc_final: 0.6345 (mmpt) REVERT: S 19 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8406 (tttt) REVERT: S 93 MET cc_start: 0.8899 (ttt) cc_final: 0.8667 (ttp) REVERT: S 137 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7845 (m) outliers start: 42 outliers final: 21 residues processed: 159 average time/residue: 0.6062 time to fit residues: 102.4821 Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 322 HIS R 295 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106468 restraints weight = 10044.685| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.02 r_work: 0.2968 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8965 Z= 0.153 Angle : 0.577 11.028 12155 Z= 0.293 Chirality : 0.042 0.189 1390 Planarity : 0.004 0.052 1521 Dihedral : 5.424 54.947 1240 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 5.00 % Allowed : 21.91 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.10 (0.25), residues: 1117 helix: -0.10 (0.27), residues: 380 sheet: -0.93 (0.28), residues: 274 loop : -0.97 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.021 0.002 TYR B 59 PHE 0.015 0.001 PHE S 27 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8962) covalent geometry : angle 0.57408 / 0.29 (12149) SS BOND : bond 0.00611 / 0.31 ( 3) SS BOND : angle 2.66460 / 1.54 ( 6) hydrogen bonds : bond 0.03594 / 2.33 ( 386) hydrogen bonds : angle 4.68483 / 3.23 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (mtp) REVERT: A 35 LYS cc_start: 0.8853 (mttp) cc_final: 0.8337 (mtmt) REVERT: A 198 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8522 (ttp) REVERT: A 243 MET cc_start: 0.8018 (ttp) cc_final: 0.7760 (mtp) REVERT: B 19 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7655 (ttp80) REVERT: B 23 LYS cc_start: 0.8539 (ttmt) cc_final: 0.7825 (tptt) REVERT: B 46 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7607 (mtt180) REVERT: B 161 SER cc_start: 0.9460 (OUTLIER) cc_final: 0.9169 (p) REVERT: B 234 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9016 (m-80) REVERT: C 47 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8201 (mt-10) REVERT: R 115 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6291 (tmm) REVERT: R 157 MET cc_start: 0.5848 (tpp) cc_final: 0.5629 (tpp) REVERT: R 245 LYS cc_start: 0.6720 (mmpt) cc_final: 0.6469 (mmpt) REVERT: R 305 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: S 19 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8478 (tttt) REVERT: S 93 MET cc_start: 0.8832 (ttt) cc_final: 0.8620 (ttp) REVERT: S 179 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7635 (mpp-170) REVERT: S 207 LEU cc_start: 0.8368 (tt) cc_final: 0.7894 (pp) outliers start: 47 outliers final: 24 residues processed: 159 average time/residue: 0.5966 time to fit residues: 100.8287 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 333 GLN R 295 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105788 restraints weight = 10072.955| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.16 r_work: 0.2997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8965 Z= 0.147 Angle : 0.578 10.610 12155 Z= 0.293 Chirality : 0.042 0.187 1390 Planarity : 0.004 0.046 1521 Dihedral : 5.385 53.490 1240 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 5.21 % Allowed : 22.34 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1117 helix: 0.01 (0.27), residues: 380 sheet: -0.90 (0.28), residues: 274 loop : -0.96 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.019 0.001 TYR B 59 PHE 0.015 0.001 PHE S 27 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8962) covalent geometry : angle 0.57547 / 0.29 (12149) SS BOND : bond 0.00567 / 0.29 ( 3) SS BOND : angle 2.60845 / 1.51 ( 6) hydrogen bonds : bond 0.03563 / 2.31 ( 386) hydrogen bonds : angle 4.66439 / 3.22 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: A 35 LYS cc_start: 0.8817 (mttp) cc_final: 0.8286 (mtmt) REVERT: A 198 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (ttp) REVERT: A 261 ASP cc_start: 0.8377 (p0) cc_final: 0.8012 (p0) REVERT: B 19 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7620 (ttp80) REVERT: B 23 LYS cc_start: 0.8498 (ttmt) cc_final: 0.7768 (tptt) REVERT: B 46 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7559 (mtt180) REVERT: B 161 SER cc_start: 0.9486 (OUTLIER) cc_final: 0.9205 (p) REVERT: B 217 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7253 (pp-130) REVERT: B 234 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.8994 (m-80) REVERT: B 300 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8666 (mt) REVERT: C 47 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8194 (mt-10) REVERT: R 115 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6208 (tmm) REVERT: R 157 MET cc_start: 0.5800 (tpp) cc_final: 0.5593 (tpp) REVERT: R 169 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7029 (tp) REVERT: R 245 LYS cc_start: 0.6646 (mmpt) cc_final: 0.6394 (mmpt) REVERT: R 305 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: S 19 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8504 (tttt) REVERT: S 93 MET cc_start: 0.8813 (ttt) cc_final: 0.8593 (ttp) REVERT: S 179 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7641 (mpp-170) outliers start: 49 outliers final: 29 residues processed: 156 average time/residue: 0.5904 time to fit residues: 98.0409 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105581 restraints weight = 9981.036| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.16 r_work: 0.3037 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8965 Z= 0.147 Angle : 0.578 10.610 12155 Z= 0.293 Chirality : 0.042 0.187 1390 Planarity : 0.004 0.046 1521 Dihedral : 5.385 53.490 1240 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 4.68 % Allowed : 23.19 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1117 helix: 0.01 (0.27), residues: 380 sheet: -0.90 (0.28), residues: 274 loop : -0.96 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.019 0.001 TYR B 59 PHE 0.015 0.001 PHE S 27 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8962) covalent geometry : angle 0.57547 / 0.29 (12149) SS BOND : bond 0.00567 / 0.29 ( 3) SS BOND : angle 2.60845 / 1.51 ( 6) hydrogen bonds : bond 0.03563 / 2.31 ( 386) hydrogen bonds : angle 4.66439 / 3.22 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: A 35 LYS cc_start: 0.8844 (mttp) cc_final: 0.8338 (mtmt) REVERT: A 198 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8551 (ttp) REVERT: A 261 ASP cc_start: 0.8384 (p0) cc_final: 0.8029 (p0) REVERT: B 19 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7675 (ttp80) REVERT: B 23 LYS cc_start: 0.8538 (ttmt) cc_final: 0.7824 (tptt) REVERT: B 46 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7622 (mtt180) REVERT: B 161 SER cc_start: 0.9481 (OUTLIER) cc_final: 0.9195 (p) REVERT: B 217 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7340 (pp-130) REVERT: B 234 PHE cc_start: 0.9493 (OUTLIER) cc_final: 0.9017 (m-80) REVERT: B 300 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8668 (mt) REVERT: C 47 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8199 (mt-10) REVERT: R 115 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6288 (tmm) REVERT: R 157 MET cc_start: 0.5866 (tpp) cc_final: 0.5649 (tpp) REVERT: R 169 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7055 (tp) REVERT: R 245 LYS cc_start: 0.6717 (mmpt) cc_final: 0.6467 (mmpt) REVERT: R 305 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: S 19 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8536 (tttt) REVERT: S 93 MET cc_start: 0.8814 (ttt) cc_final: 0.8612 (ttp) REVERT: S 179 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7659 (mpp-170) outliers start: 44 outliers final: 30 residues processed: 149 average time/residue: 0.5801 time to fit residues: 91.8405 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 331 ASN A 333 GLN R 295 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107139 restraints weight = 9970.790| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.16 r_work: 0.3044 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8965 Z= 0.125 Angle : 0.577 10.761 12155 Z= 0.290 Chirality : 0.042 0.188 1390 Planarity : 0.004 0.046 1521 Dihedral : 5.297 52.594 1240 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 4.57 % Allowed : 23.40 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1117 helix: 0.15 (0.27), residues: 381 sheet: -0.93 (0.28), residues: 276 loop : -0.91 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.018 0.001 TYR A 296 PHE 0.015 0.001 PHE S 27 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8962) covalent geometry : angle 0.57436 / 0.29 (12149) SS BOND : bond 0.00559 / 0.29 ( 3) SS BOND : angle 2.63346 / 1.52 ( 6) hydrogen bonds : bond 0.03446 / 2.24 ( 386) hydrogen bonds : angle 4.60532 / 3.19 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8471 (mtp) REVERT: A 35 LYS cc_start: 0.8832 (mttp) cc_final: 0.8341 (mtmt) REVERT: A 198 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8543 (ttp) REVERT: A 229 ASP cc_start: 0.7281 (p0) cc_final: 0.7023 (p0) REVERT: A 243 MET cc_start: 0.7590 (ttm) cc_final: 0.7174 (mtm) REVERT: A 261 ASP cc_start: 0.8384 (p0) cc_final: 0.8023 (p0) REVERT: B 19 ARG cc_start: 0.7957 (ttp-170) cc_final: 0.7667 (ttp80) REVERT: B 23 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7831 (tptt) REVERT: B 46 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7615 (mtt180) REVERT: B 161 SER cc_start: 0.9463 (OUTLIER) cc_final: 0.9170 (p) REVERT: B 234 PHE cc_start: 0.9463 (OUTLIER) cc_final: 0.9044 (m-80) REVERT: B 300 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 47 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8206 (mt-10) REVERT: R 115 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6063 (tmm) REVERT: R 157 MET cc_start: 0.5808 (tpp) cc_final: 0.5565 (tpp) REVERT: R 169 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7076 (tp) REVERT: R 245 LYS cc_start: 0.6706 (mmpt) cc_final: 0.6459 (mmpt) REVERT: S 11 LEU cc_start: 0.8835 (mm) cc_final: 0.7986 (mm) REVERT: S 19 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8557 (tttt) REVERT: S 207 LEU cc_start: 0.8364 (tt) cc_final: 0.7966 (pp) outliers start: 43 outliers final: 23 residues processed: 154 average time/residue: 0.5904 time to fit residues: 96.5742 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106563 restraints weight = 10046.594| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.12 r_work: 0.2975 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8965 Z= 0.127 Angle : 0.576 10.690 12155 Z= 0.289 Chirality : 0.042 0.184 1390 Planarity : 0.004 0.046 1521 Dihedral : 5.372 52.647 1240 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 3.72 % Allowed : 24.26 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1117 helix: 0.16 (0.27), residues: 381 sheet: -0.93 (0.28), residues: 276 loop : -0.91 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.017 0.001 TYR B 59 PHE 0.015 0.001 PHE S 27 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8962) covalent geometry : angle 0.57311 / 0.29 (12149) SS BOND : bond 0.00553 / 0.28 ( 3) SS BOND : angle 2.63202 / 1.52 ( 6) hydrogen bonds : bond 0.03446 / 2.24 ( 386) hydrogen bonds : angle 4.60525 / 3.19 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: A 35 LYS cc_start: 0.8800 (mttp) cc_final: 0.8290 (mtmt) REVERT: A 198 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8479 (ttp) REVERT: A 261 ASP cc_start: 0.8340 (p0) cc_final: 0.7971 (p0) REVERT: B 19 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7580 (ttp80) REVERT: B 23 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7756 (tptt) REVERT: B 46 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7534 (mtt180) REVERT: B 161 SER cc_start: 0.9451 (OUTLIER) cc_final: 0.9158 (p) REVERT: B 234 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9010 (m-80) REVERT: B 300 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 47 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8214 (mt-10) REVERT: R 115 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.5973 (tmm) REVERT: R 157 MET cc_start: 0.5776 (tpp) cc_final: 0.5537 (tpp) REVERT: R 169 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7044 (tp) REVERT: R 245 LYS cc_start: 0.6603 (mmpt) cc_final: 0.6354 (mmpt) REVERT: R 305 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: S 11 LEU cc_start: 0.8825 (mm) cc_final: 0.7974 (mm) REVERT: S 19 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8517 (tttt) REVERT: S 207 LEU cc_start: 0.8284 (tt) cc_final: 0.7871 (pp) outliers start: 35 outliers final: 23 residues processed: 149 average time/residue: 0.6209 time to fit residues: 98.2171 Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 105 optimal weight: 0.0030 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 333 GLN R 295 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108033 restraints weight = 9962.545| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.11 r_work: 0.2977 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8965 Z= 0.122 Angle : 0.576 11.287 12155 Z= 0.289 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.047 1521 Dihedral : 5.225 52.395 1240 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 4.04 % Allowed : 23.83 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.77 (0.25), residues: 1117 helix: 0.35 (0.27), residues: 379 sheet: -0.86 (0.29), residues: 276 loop : -0.86 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.016 0.001 TYR A 296 PHE 0.015 0.001 PHE S 27 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8962) covalent geometry : angle 0.57282 / 0.29 (12149) SS BOND : bond 0.00554 / 0.28 ( 3) SS BOND : angle 2.65942 / 1.54 ( 6) hydrogen bonds : bond 0.03371 / 2.19 ( 386) hydrogen bonds : angle 4.55420 / 3.15 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.19 seconds wall clock time: 65 minutes 23.95 seconds (3923.95 seconds total)