Starting phenix.real_space_refine on Tue Mar 3 22:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kpf_0744/03_2026/6kpf_0744.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kpf_0744/03_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_0744/03_2026/6kpf_0744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kpf_0744/03_2026/6kpf_0744.map" model { file = "/net/cci-nas-00/data/ceres_data/6kpf_0744/03_2026/6kpf_0744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kpf_0744/03_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-dev-5986/lib/python3.9/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: 1.62, per 1000 atoms: 0.18 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: 0.53 Conformation dependent library (CDL) restraints added in 341.2 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: 0.20 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: 1.03 Time building geometry restraints manager: 0.76 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: 4759 18.06 - 36.12: 469 36.12 - 54.18: 84 54.18 - 72.24: 12 72.24 - 90.30: 9 Dihedral angle restraints: 5333 sinusoidal: 2049 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 5330 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 14.925 90.302 3206 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 covalent geometry : bond 0.00683 ( 8962) covalent geometry : angle 0.90873 (12149) SS BOND : bond 0.01118 ( 3) SS BOND : angle 1.53984 ( 6) hydrogen bonds : bond 0.27140 ( 386) hydrogen bonds : angle 10.35930 ( 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 : 0.341 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: 0.6508 time to fit residues: 109.4057 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 : 0.342 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 244 HIS A 269 ASN A 322 HIS B 32 GLN B 62 HIS B 175 GLN B 340 ASN C 18 GLN R 295 ASN S 3 GLN S 182 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104816 restraints weight = 10108.470| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.19 r_work: 0.2915 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1504 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= 0.203 Angle : 0.641 10.698 12155 Z= 0.339 Chirality : 0.044 0.169 1390 Planarity : 0.006 0.074 1521 Dihedral : 6.011 58.649 1264 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.40 % Favored : 96.42 % Rotamer: Outliers : 2.66 % Allowed : 17.66 % Favored : 79.68 % 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: -2.95 (0.22), residues: 1117 helix: -2.62 (0.20), residues: 378 sheet: -1.11 (0.28), residues: 282 loop : -1.69 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.025 0.002 TYR S 178 PHE 0.016 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 covalent geometry : bond 0.00448 ( 8962) covalent geometry : angle 0.63977 (12149) SS BOND : bond 0.00657 ( 3) SS BOND : angle 1.94657 ( 6) hydrogen bonds : bond 0.05245 ( 386) hydrogen bonds : angle 5.70758 ( 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 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8652 (ttp) cc_final: 0.8272 (mtp) REVERT: A 21 ARG cc_start: 0.8242 (ttp80) cc_final: 0.8029 (ttp-110) REVERT: A 35 LYS cc_start: 0.8805 (mttp) cc_final: 0.8172 (mtmt) REVERT: A 198 MET cc_start: 0.8693 (mtm) cc_final: 0.8416 (ttp) REVERT: B 23 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7716 (tptt) REVERT: B 325 MET cc_start: 0.9080 (tpp) cc_final: 0.8845 (tpp) REVERT: C 47 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8255 (mt-10) REVERT: C 53 PRO cc_start: 0.7187 (Cg_exo) cc_final: 0.6985 (Cg_endo) REVERT: R 71 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7300 (mm) REVERT: R 157 MET cc_start: 0.5734 (tpp) cc_final: 0.5496 (tpp) outliers start: 25 outliers final: 8 residues processed: 150 average time/residue: 0.6690 time to fit residues: 105.8729 Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 S residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 91 HIS B 119 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 = 0.160055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106028 restraints weight = 9957.992| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.12 r_work: 0.2943 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1881 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= 0.158 Angle : 0.588 10.789 12155 Z= 0.306 Chirality : 0.042 0.164 1390 Planarity : 0.005 0.067 1521 Dihedral : 5.676 59.702 1264 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 3.72 % Allowed : 19.47 % Favored : 76.81 % 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: -2.12 (0.23), residues: 1117 helix: -1.43 (0.25), residues: 382 sheet: -1.10 (0.28), residues: 278 loop : -1.36 (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 A 189 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8962) covalent geometry : angle 0.58660 (12149) SS BOND : bond 0.00690 ( 3) SS BOND : angle 1.86957 ( 6) hydrogen bonds : bond 0.04074 ( 386) hydrogen bonds : angle 5.12135 ( 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 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8659 (ttp) cc_final: 0.8317 (mtp) REVERT: A 35 LYS cc_start: 0.8835 (mttp) cc_final: 0.8245 (mtmt) REVERT: A 198 MET cc_start: 0.8712 (mtm) cc_final: 0.8447 (ttp) REVERT: B 23 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7757 (tptt) REVERT: B 161 SER cc_start: 0.9495 (p) cc_final: 0.9269 (p) REVERT: B 234 PHE cc_start: 0.9518 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: B 300 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8721 (mt) REVERT: C 20 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7964 (ttpt) REVERT: C 46 LYS cc_start: 0.8564 (mmtm) cc_final: 0.7864 (mmtt) REVERT: C 47 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 53 PRO cc_start: 0.7178 (Cg_exo) cc_final: 0.6950 (Cg_endo) REVERT: R 71 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7126 (mm) REVERT: R 115 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6202 (tmm) REVERT: R 245 LYS cc_start: 0.6614 (mmpt) cc_final: 0.6359 (mmpt) REVERT: R 286 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4988 (mtp) REVERT: R 293 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7084 (ptt) REVERT: S 93 MET cc_start: 0.8946 (ttt) cc_final: 0.8697 (ttp) outliers start: 35 outliers final: 15 residues processed: 152 average time/residue: 0.6506 time to fit residues: 104.7025 Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 20 LYS 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: 8.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105441 restraints weight = 10184.851| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.13 r_work: 0.2952 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8965 Z= 0.175 Angle : 0.589 10.998 12155 Z= 0.304 Chirality : 0.043 0.163 1390 Planarity : 0.004 0.065 1521 Dihedral : 5.596 59.254 1264 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 4.26 % Allowed : 19.57 % Favored : 76.17 % 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: -1.73 (0.24), residues: 1117 helix: -0.91 (0.26), residues: 382 sheet: -1.05 (0.28), residues: 278 loop : -1.21 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 190 TYR 0.021 0.002 TYR S 178 PHE 0.015 0.001 PHE S 27 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8962) covalent geometry : angle 0.58824 (12149) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.81346 ( 6) hydrogen bonds : bond 0.03932 ( 386) hydrogen bonds : angle 4.96899 ( 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 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (mtp) REVERT: A 21 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8002 (ttp80) REVERT: A 35 LYS cc_start: 0.8854 (mttp) cc_final: 0.8271 (mtmt) REVERT: A 198 MET cc_start: 0.8706 (mtm) cc_final: 0.8427 (ttp) REVERT: A 243 MET cc_start: 0.7628 (ttm) cc_final: 0.7152 (mtm) REVERT: B 23 LYS cc_start: 0.8500 (ttmt) cc_final: 0.7776 (tptt) REVERT: B 161 SER cc_start: 0.9501 (p) cc_final: 0.9241 (p) REVERT: B 234 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: B 300 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (mt) REVERT: C 20 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7944 (mtmm) REVERT: C 47 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 53 PRO cc_start: 0.7136 (Cg_exo) cc_final: 0.6899 (Cg_endo) REVERT: R 71 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7117 (mm) REVERT: R 115 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: R 157 MET cc_start: 0.5631 (tpp) cc_final: 0.5339 (tpp) REVERT: R 169 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6883 (pt) REVERT: R 245 LYS cc_start: 0.6642 (mmpt) cc_final: 0.6380 (mmpt) REVERT: R 286 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.5015 (mtp) REVERT: S 11 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8547 (mm) REVERT: S 93 MET cc_start: 0.8925 (ttt) cc_final: 0.8692 (ttp) REVERT: S 137 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7858 (m) outliers start: 40 outliers final: 19 residues processed: 156 average time/residue: 0.6828 time to fit residues: 112.5902 Evaluate side-chains 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR 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 300 LEU Chi-restraints excluded: chain C residue 20 LYS 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 169 LEU 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 11 LEU 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 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: 7.9990 chunk 80 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101974 restraints weight = 10027.695| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.18 r_work: 0.2948 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8965 Z= 0.242 Angle : 0.638 11.459 12155 Z= 0.328 Chirality : 0.045 0.188 1390 Planarity : 0.004 0.063 1521 Dihedral : 5.777 59.399 1264 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Rotamer: Outliers : 4.68 % Allowed : 20.74 % Favored : 74.57 % 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: -1.50 (0.24), residues: 1117 helix: -0.55 (0.26), residues: 375 sheet: -1.05 (0.28), residues: 280 loop : -1.15 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.026 0.002 TYR S 178 PHE 0.017 0.002 PHE S 27 TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8962) covalent geometry : angle 0.63524 (12149) SS BOND : bond 0.00444 ( 3) SS BOND : angle 2.60473 ( 6) hydrogen bonds : bond 0.04059 ( 386) hydrogen bonds : angle 4.99035 ( 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 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.335 Fit side-chains REVERT: A 18 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: A 35 LYS cc_start: 0.8915 (mttp) cc_final: 0.8371 (mtmt) REVERT: A 198 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8549 (ttp) REVERT: B 23 LYS cc_start: 0.8510 (ttmt) cc_final: 0.7761 (tptt) REVERT: B 46 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7644 (mtt180) REVERT: B 130 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 161 SER cc_start: 0.9516 (p) cc_final: 0.9263 (p) REVERT: B 234 PHE cc_start: 0.9571 (OUTLIER) cc_final: 0.9006 (m-80) REVERT: C 20 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: C 47 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8223 (mt-10) REVERT: C 53 PRO cc_start: 0.7146 (Cg_exo) cc_final: 0.6910 (Cg_endo) REVERT: R 115 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6401 (tmm) REVERT: R 157 MET cc_start: 0.5694 (tpp) cc_final: 0.5428 (tpp) REVERT: R 169 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7142 (pt) REVERT: R 245 LYS cc_start: 0.6676 (mmpt) cc_final: 0.6422 (mmpt) REVERT: R 286 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5153 (mtp) REVERT: R 305 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: S 137 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7871 (m) outliers start: 44 outliers final: 19 residues processed: 159 average time/residue: 0.6380 time to fit residues: 107.4786 Evaluate side-chains 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 189 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 C residue 20 LYS 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 169 LEU 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 115 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: 0.5980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.0040 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 295 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.160598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106369 restraints weight = 9987.202| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.16 r_work: 0.2974 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2249 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= 0.129 Angle : 0.565 11.219 12155 Z= 0.288 Chirality : 0.042 0.189 1390 Planarity : 0.004 0.061 1521 Dihedral : 5.425 55.144 1264 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.69 % Rotamer: Outliers : 4.36 % Allowed : 21.81 % Favored : 73.83 % 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: -1.16 (0.25), residues: 1117 helix: -0.21 (0.27), residues: 379 sheet: -0.92 (0.28), residues: 274 loop : -0.98 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.016 0.001 TYR S 178 PHE 0.016 0.001 PHE S 27 TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8962) covalent geometry : angle 0.56239 (12149) SS BOND : bond 0.00580 ( 3) SS BOND : angle 2.67329 ( 6) hydrogen bonds : bond 0.03549 ( 386) hydrogen bonds : angle 4.71819 ( 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 184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8370 (mtp) REVERT: A 35 LYS cc_start: 0.8807 (mttp) cc_final: 0.8270 (mtmt) REVERT: A 198 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: B 19 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7568 (ttp80) REVERT: B 23 LYS cc_start: 0.8479 (ttmt) cc_final: 0.7752 (tptt) REVERT: B 46 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7573 (mtt180) REVERT: B 161 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9149 (p) REVERT: B 234 PHE cc_start: 0.9474 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: C 20 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: C 47 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 53 PRO cc_start: 0.7066 (Cg_exo) cc_final: 0.6829 (Cg_endo) REVERT: R 115 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6200 (tmm) REVERT: R 245 LYS cc_start: 0.6565 (mmpt) cc_final: 0.6318 (mmpt) REVERT: S 19 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8363 (tttt) REVERT: S 93 MET cc_start: 0.8829 (ttt) cc_final: 0.8618 (ttp) REVERT: S 207 LEU cc_start: 0.8284 (tt) cc_final: 0.7821 (pp) outliers start: 41 outliers final: 21 residues processed: 171 average time/residue: 0.5955 time to fit residues: 108.2885 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 20 LYS 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 249 LEU Chi-restraints excluded: chain R residue 271 THR 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 138 THR 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: 4.9990 chunk 40 optimal weight: 0.0060 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 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 = 0.3798 r_free = 0.3798 target = 0.160769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106987 restraints weight = 10095.915| |-----------------------------------------------------------------------------| r_work (start): 0.3208 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: 0.8105 moved from start: 0.2373 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= 0.124 Angle : 0.566 10.979 12155 Z= 0.286 Chirality : 0.042 0.188 1390 Planarity : 0.004 0.052 1521 Dihedral : 5.270 52.643 1264 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.69 % Rotamer: Outliers : 4.47 % Allowed : 23.30 % Favored : 72.23 % 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: -0.96 (0.25), residues: 1117 helix: 0.05 (0.27), residues: 380 sheet: -0.89 (0.28), residues: 276 loop : -0.88 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 87 TYR 0.016 0.001 TYR S 178 PHE 0.014 0.001 PHE S 27 TRP 0.016 0.001 TRP B 211 HIS 0.002 0.001 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8962) covalent geometry : angle 0.56336 (12149) SS BOND : bond 0.00574 ( 3) SS BOND : angle 2.62569 ( 6) hydrogen bonds : bond 0.03452 ( 386) hydrogen bonds : angle 4.61533 ( 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: 42 poor density : 134 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: A 35 LYS cc_start: 0.8847 (mttp) cc_final: 0.8353 (mtmt) REVERT: A 198 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8535 (ttp) REVERT: A 229 ASP cc_start: 0.7260 (p0) cc_final: 0.7030 (p0) REVERT: B 19 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7652 (ttp80) REVERT: B 23 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7815 (tptt) REVERT: B 46 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7611 (mtt180) REVERT: B 161 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.9148 (p) REVERT: B 234 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.9053 (m-80) REVERT: B 300 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (mt) REVERT: C 47 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8187 (mt-10) REVERT: R 115 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6209 (tmm) REVERT: R 245 LYS cc_start: 0.6682 (mmpt) cc_final: 0.6442 (mmpt) REVERT: S 11 LEU cc_start: 0.8849 (mm) cc_final: 0.8011 (mm) REVERT: S 19 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8500 (tttt) REVERT: S 93 MET cc_start: 0.8794 (ttt) cc_final: 0.8593 (ttp) REVERT: S 207 LEU cc_start: 0.8352 (tt) cc_final: 0.7880 (pp) outliers start: 42 outliers final: 22 residues processed: 159 average time/residue: 0.6477 time to fit residues: 108.9639 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 242 ARG 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 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 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 105 VAL Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR 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 138 THR 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: 0.5980 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 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 = 0.3792 r_free = 0.3792 target = 0.160096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106417 restraints weight = 10000.712| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.13 r_work: 0.3064 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2409 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= 0.151 Angle : 0.582 10.653 12155 Z= 0.294 Chirality : 0.043 0.187 1390 Planarity : 0.004 0.047 1521 Dihedral : 5.295 52.729 1264 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 4.26 % Allowed : 24.04 % Favored : 71.70 % 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: -0.85 (0.25), residues: 1117 helix: 0.15 (0.27), residues: 381 sheet: -0.83 (0.29), residues: 274 loop : -0.84 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.019 0.001 TYR S 178 PHE 0.015 0.001 PHE S 27 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8962) covalent geometry : angle 0.57911 (12149) SS BOND : bond 0.00550 ( 3) SS BOND : angle 2.65081 ( 6) hydrogen bonds : bond 0.03527 ( 386) hydrogen bonds : angle 4.60784 ( 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 171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.372 Fit side-chains REVERT: A 18 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (mtp) REVERT: A 35 LYS cc_start: 0.8850 (mttp) cc_final: 0.8354 (mtmt) REVERT: A 261 ASP cc_start: 0.8384 (p0) cc_final: 0.7963 (p0) REVERT: B 19 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7656 (ttp80) REVERT: B 23 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7840 (tptt) REVERT: B 46 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7630 (mtt180) REVERT: B 161 SER cc_start: 0.9459 (OUTLIER) cc_final: 0.9178 (p) REVERT: B 217 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7340 (pp-130) REVERT: B 234 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9077 (m-80) REVERT: B 300 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8510 (mt) REVERT: C 47 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8165 (mt-10) REVERT: R 115 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6103 (tmm) REVERT: R 169 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7053 (tp) REVERT: R 245 LYS cc_start: 0.6655 (mmpt) cc_final: 0.6432 (mmpt) REVERT: S 11 LEU cc_start: 0.8844 (mm) cc_final: 0.8017 (mm) REVERT: S 19 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8529 (tttt) REVERT: S 179 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6527 (mtp180) outliers start: 40 outliers final: 23 residues processed: 155 average time/residue: 0.6321 time to fit residues: 103.8727 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain A residue 316 THR 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 300 LEU Chi-restraints excluded: chain B residue 322 ASP 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 186 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR 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 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: 0.9980 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107082 restraints weight = 10001.242| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.01 r_work: 0.2970 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2452 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= 0.142 Angle : 0.590 10.727 12155 Z= 0.295 Chirality : 0.042 0.186 1390 Planarity : 0.004 0.047 1521 Dihedral : 5.289 52.717 1264 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.31 % Favored : 96.51 % Rotamer: Outliers : 4.68 % Allowed : 24.15 % Favored : 71.17 % 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: -0.81 (0.25), residues: 1117 helix: 0.22 (0.27), residues: 381 sheet: -0.85 (0.28), residues: 274 loop : -0.82 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.019 0.001 TYR A 296 PHE 0.015 0.001 PHE S 27 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8962) covalent geometry : angle 0.58740 (12149) SS BOND : bond 0.00545 ( 3) SS BOND : angle 2.64992 ( 6) hydrogen bonds : bond 0.03473 ( 386) hydrogen bonds : angle 4.60259 ( 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 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.330 Fit side-chains REVERT: A 18 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: A 35 LYS cc_start: 0.8822 (mttp) cc_final: 0.8290 (mtmt) REVERT: A 242 ARG cc_start: 0.6441 (mmt180) cc_final: 0.6226 (mmt180) REVERT: A 261 ASP cc_start: 0.8353 (p0) cc_final: 0.7922 (p0) REVERT: A 273 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 19 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7575 (ttp80) REVERT: B 23 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7761 (tptt) REVERT: B 46 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7542 (mtt180) REVERT: B 161 SER cc_start: 0.9437 (OUTLIER) cc_final: 0.9152 (p) REVERT: B 217 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7204 (pp-130) REVERT: B 234 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9029 (m-80) REVERT: C 47 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8146 (mt-10) REVERT: R 115 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6013 (tmm) REVERT: R 245 LYS cc_start: 0.6559 (mmpt) cc_final: 0.6334 (mmpt) REVERT: S 11 LEU cc_start: 0.8821 (mm) cc_final: 0.7992 (mm) REVERT: S 19 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8493 (tttt) REVERT: S 179 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6481 (mtp180) REVERT: S 207 LEU cc_start: 0.8309 (tt) cc_final: 0.7869 (pp) outliers start: 44 outliers final: 27 residues processed: 158 average time/residue: 0.6299 time to fit residues: 105.4304 Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR 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 303 ASP Chi-restraints excluded: chain B residue 322 ASP 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 186 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3789 r_free = 0.3789 target = 0.159964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106215 restraints weight = 10073.239| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.15 r_work: 0.2962 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2433 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= 0.142 Angle : 0.590 10.727 12155 Z= 0.295 Chirality : 0.042 0.186 1390 Planarity : 0.004 0.047 1521 Dihedral : 5.289 52.717 1264 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.31 % Favored : 96.51 % Rotamer: Outliers : 3.94 % Allowed : 24.47 % Favored : 71.60 % 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: -0.81 (0.25), residues: 1117 helix: 0.22 (0.27), residues: 381 sheet: -0.85 (0.28), residues: 274 loop : -0.82 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.019 0.001 TYR A 296 PHE 0.015 0.001 PHE S 27 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8962) covalent geometry : angle 0.58740 (12149) SS BOND : bond 0.00545 ( 3) SS BOND : angle 2.64992 ( 6) hydrogen bonds : bond 0.03473 ( 386) hydrogen bonds : angle 4.60259 ( 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 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.251 Fit side-chains REVERT: A 18 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: A 35 LYS cc_start: 0.8819 (mttp) cc_final: 0.8282 (mtmt) REVERT: A 242 ARG cc_start: 0.6424 (mmt180) cc_final: 0.6199 (mmt180) REVERT: A 261 ASP cc_start: 0.8367 (p0) cc_final: 0.7934 (p0) REVERT: A 273 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 19 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7555 (ttp80) REVERT: B 23 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7740 (tptt) REVERT: B 46 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7544 (mtt180) REVERT: B 161 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9172 (p) REVERT: B 217 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7189 (pp-130) REVERT: B 234 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9032 (m-80) REVERT: C 47 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8151 (mt-10) REVERT: R 115 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.5980 (tmm) REVERT: R 245 LYS cc_start: 0.6533 (mmpt) cc_final: 0.6311 (mmpt) REVERT: S 11 LEU cc_start: 0.8821 (mm) cc_final: 0.7990 (mm) REVERT: S 19 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8489 (tttt) REVERT: S 179 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6506 (mtp180) REVERT: S 207 LEU cc_start: 0.8311 (tt) cc_final: 0.7856 (pp) outliers start: 37 outliers final: 27 residues processed: 152 average time/residue: 0.6756 time to fit residues: 108.3903 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR 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 303 ASP Chi-restraints excluded: chain B residue 322 ASP 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 186 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 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 = 0.3790 r_free = 0.3790 target = 0.160103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106434 restraints weight = 9988.470| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.15 r_work: 0.3045 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8965 Z= 0.146 Angle : 0.595 10.650 12155 Z= 0.296 Chirality : 0.042 0.188 1390 Planarity : 0.004 0.047 1521 Dihedral : 5.276 52.534 1264 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.40 % Favored : 96.42 % Rotamer: Outliers : 4.15 % Allowed : 24.36 % Favored : 71.49 % 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: -0.78 (0.25), residues: 1117 helix: 0.29 (0.27), residues: 381 sheet: -0.86 (0.28), residues: 277 loop : -0.82 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.019 0.001 TYR S 178 PHE 0.016 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 covalent geometry : bond 0.00330 ( 8962) covalent geometry : angle 0.59240 (12149) SS BOND : bond 0.00537 ( 3) SS BOND : angle 2.65804 ( 6) hydrogen bonds : bond 0.03454 ( 386) hydrogen bonds : angle 4.59572 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4142.69 seconds wall clock time: 71 minutes 10.01 seconds (4270.01 seconds total)