Starting phenix.real_space_refine on Thu Mar 13 03:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.map" model { file = "/net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkx_24506/03_2025/7rkx_24506.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 59 5.16 5 C 5443 2.51 5 N 1456 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8559 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1759 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1780 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1991 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Time building chain proxies: 5.25, per 1000 atoms: 0.61 Number of scatterers: 8559 At special positions: 0 Unit cell: (92.8439, 125.816, 132.758, 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 59 16.00 O 1601 8.00 N 1456 7.00 C 5443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 176 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 997.8 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.723A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.583A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.549A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.953A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.644A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.616A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.578A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.635A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.896A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 33 Processing helix chain 'R' and resid 36 through 57 removed outlier: 3.581A pdb=" N MET R 40 " --> pdb=" O GLY R 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 64 removed outlier: 3.904A pdb=" N LYS R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.947A pdb=" N THR R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR R 69 " --> pdb=" O PRO R 65 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 81 " --> pdb=" O ASP R 77 " (cutoff:3.500A) Proline residue: R 85 - end of helix removed outlier: 3.554A pdb=" N LEU R 88 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 133 removed outlier: 3.964A pdb=" N SER R 104 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 108 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS R 109 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL R 131 " --> pdb=" O ASP R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 162 removed outlier: 3.603A pdb=" N GLY R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 167 removed outlier: 4.824A pdb=" N LEU R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 201 through 223 removed outlier: 3.666A pdb=" N ALA R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR R 222 " --> pdb=" O PHE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 245 removed outlier: 3.669A pdb=" N HIS R 232 " --> pdb=" O MET R 228 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.621A pdb=" N ASN R 249 " --> pdb=" O TRP R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 290 removed outlier: 3.634A pdb=" N VAL R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 298 removed outlier: 3.689A pdb=" N ILE R 295 " --> pdb=" O PRO R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.587A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.821A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.655A 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: 7.017A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.120A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.872A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.279A 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: 3.512A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.586A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.799A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 removed outlier: 5.890A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.500A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.581A pdb=" N PHE D 200 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.160A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.160A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR D 226 " --> pdb=" O GLN D 219 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2771 1.34 - 1.46: 2106 1.46 - 1.58: 3779 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 8739 Sorted by residual: bond pdb=" CG LEU R 276 " pdb=" CD2 LEU R 276 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" N GLY R 262 " pdb=" CA GLY R 262 " ideal model delta sigma weight residual 1.444 1.454 -0.011 1.02e-02 9.61e+03 1.07e+00 bond pdb=" C LEU R 84 " pdb=" N PRO R 85 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.30e-02 5.92e+03 1.01e+00 bond pdb=" CA ASP A 193 " pdb=" CB ASP A 193 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.51e-02 4.39e+03 9.99e-01 ... (remaining 8734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11676 2.24 - 4.48: 160 4.48 - 6.72: 29 6.72 - 8.95: 4 8.95 - 11.19: 1 Bond angle restraints: 11870 Sorted by residual: angle pdb=" N GLY R 262 " pdb=" CA GLY R 262 " pdb=" C GLY R 262 " ideal model delta sigma weight residual 111.18 116.31 -5.13 1.54e+00 4.22e-01 1.11e+01 angle pdb=" CA LEU R 276 " pdb=" CB LEU R 276 " pdb=" CG LEU R 276 " ideal model delta sigma weight residual 116.30 127.49 -11.19 3.50e+00 8.16e-02 1.02e+01 angle pdb=" N LEU R 276 " pdb=" CA LEU R 276 " pdb=" CB LEU R 276 " ideal model delta sigma weight residual 110.28 115.13 -4.85 1.55e+00 4.16e-01 9.79e+00 angle pdb=" C LYS A 192 " pdb=" N ASP A 193 " pdb=" CA ASP A 193 " ideal model delta sigma weight residual 122.61 127.34 -4.73 1.56e+00 4.11e-01 9.18e+00 angle pdb=" CA CYS D 96 " pdb=" CB CYS D 96 " pdb=" SG CYS D 96 " ideal model delta sigma weight residual 114.40 120.57 -6.17 2.30e+00 1.89e-01 7.20e+00 ... (remaining 11865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4673 15.81 - 31.61: 353 31.61 - 47.42: 84 47.42 - 63.23: 13 63.23 - 79.04: 6 Dihedral angle restraints: 5129 sinusoidal: 1868 harmonic: 3261 Sorted by residual: dihedral pdb=" CA SER B 227 " pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS R 103 " pdb=" SG CYS R 103 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -121.37 35.37 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1002 0.051 - 0.102: 288 0.102 - 0.152: 61 0.152 - 0.203: 4 0.203 - 0.254: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA LEU R 84 " pdb=" N LEU R 84 " pdb=" C LEU R 84 " pdb=" CB LEU R 84 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP A 193 " pdb=" N ASP A 193 " pdb=" C ASP A 193 " pdb=" CB ASP A 193 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1353 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 84 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO R 85 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO R 85 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 85 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 110 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE R 110 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE R 110 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR R 111 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 109 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C CYS R 109 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS R 109 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE R 110 " -0.017 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 154 2.69 - 3.24: 7963 3.24 - 3.79: 12285 3.79 - 4.35: 16174 4.35 - 4.90: 28553 Nonbonded interactions: 65129 Sorted by model distance: nonbonded pdb=" O SER B 227 " pdb=" OG SER B 245 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR R 201 " pdb=" O ALA R 242 " model vdw 2.233 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.263 3.120 nonbonded pdb=" NE2 GLN C 18 " pdb=" OE2 GLU C 22 " model vdw 2.282 3.120 nonbonded pdb=" O SER D 52 " pdb=" NH1 ARG D 72 " model vdw 2.290 3.120 ... (remaining 65124 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: 8.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8739 Z= 0.326 Angle : 0.707 11.192 11870 Z= 0.384 Chirality : 0.048 0.254 1356 Planarity : 0.006 0.086 1510 Dihedral : 12.430 79.035 3020 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1106 helix: 0.27 (0.25), residues: 359 sheet: 0.24 (0.31), residues: 283 loop : -1.29 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 47 HIS 0.006 0.001 HIS D 220 PHE 0.017 0.002 PHE B 241 TYR 0.017 0.002 TYR D 178 ARG 0.006 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.059 Fit side-chains REVERT: A 25 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 305 CYS cc_start: 0.7251 (m) cc_final: 0.6958 (m) REVERT: C 58 GLU cc_start: 0.8756 (pm20) cc_final: 0.8532 (pm20) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2196 time to fit residues: 46.3003 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 269 ASN A 294 ASN A 331 ASN B 17 GLN B 32 GLN R 94 HIS ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 ASN R 197 ASN R 290 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105074 restraints weight = 11904.592| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.63 r_work: 0.3076 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8739 Z= 0.191 Angle : 0.572 9.990 11870 Z= 0.302 Chirality : 0.043 0.181 1356 Planarity : 0.004 0.058 1510 Dihedral : 4.821 73.208 1214 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.36 % Allowed : 7.84 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1106 helix: 1.35 (0.27), residues: 377 sheet: 0.44 (0.32), residues: 284 loop : -1.20 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.004 0.001 HIS D 220 PHE 0.011 0.001 PHE R 110 TYR 0.020 0.001 TYR R 57 ARG 0.003 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.556 Fit side-chains REVERT: A 25 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 186 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 217 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7972 (ptm) REVERT: C 20 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7912 (mtpt) REVERT: C 58 GLU cc_start: 0.8724 (pm20) cc_final: 0.8434 (pm20) REVERT: D 6 GLU cc_start: 0.8645 (mp0) cc_final: 0.8419 (mp0) outliers start: 12 outliers final: 7 residues processed: 136 average time/residue: 0.2988 time to fit residues: 56.0723 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 72 ASN R 94 HIS ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108267 restraints weight = 12066.821| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.73 r_work: 0.3075 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8739 Z= 0.148 Angle : 0.515 8.089 11870 Z= 0.270 Chirality : 0.041 0.150 1356 Planarity : 0.003 0.039 1510 Dihedral : 4.562 72.938 1214 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 1.25 % Allowed : 9.77 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1106 helix: 1.94 (0.28), residues: 378 sheet: 0.54 (0.32), residues: 277 loop : -0.96 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.007 0.001 HIS R 94 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR D 178 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.012 Fit side-chains REVERT: A 20 ASP cc_start: 0.8335 (m-30) cc_final: 0.7941 (m-30) REVERT: A 186 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8034 (mm-30) REVERT: B 153 ASP cc_start: 0.8531 (t0) cc_final: 0.8307 (t0) REVERT: B 217 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8193 (ptm) REVERT: C 20 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7975 (mtpt) REVERT: C 58 GLU cc_start: 0.8738 (pm20) cc_final: 0.8321 (pm20) REVERT: D 6 GLU cc_start: 0.8564 (mp0) cc_final: 0.8306 (mp0) outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 0.1995 time to fit residues: 37.0075 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105614 restraints weight = 12058.161| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.70 r_work: 0.3036 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8739 Z= 0.215 Angle : 0.545 7.668 11870 Z= 0.286 Chirality : 0.042 0.154 1356 Planarity : 0.003 0.031 1510 Dihedral : 4.638 70.770 1214 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 1.82 % Allowed : 12.61 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1106 helix: 2.04 (0.28), residues: 378 sheet: 0.54 (0.32), residues: 274 loop : -0.94 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS R 94 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR R 57 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.925 Fit side-chains REVERT: A 20 ASP cc_start: 0.8431 (m-30) cc_final: 0.8010 (m-30) REVERT: B 153 ASP cc_start: 0.8559 (t0) cc_final: 0.8330 (t0) REVERT: B 217 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: C 20 LYS cc_start: 0.8232 (ttpp) cc_final: 0.8020 (mtpt) REVERT: C 58 GLU cc_start: 0.8783 (pm20) cc_final: 0.8316 (pm20) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2088 time to fit residues: 38.9876 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107689 restraints weight = 12008.421| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.72 r_work: 0.3075 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8739 Z= 0.144 Angle : 0.504 8.081 11870 Z= 0.263 Chirality : 0.041 0.212 1356 Planarity : 0.003 0.031 1510 Dihedral : 4.463 72.328 1214 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 2.27 % Allowed : 13.75 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1106 helix: 2.20 (0.28), residues: 375 sheet: 0.81 (0.32), residues: 264 loop : -0.89 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.006 0.001 HIS R 94 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR D 178 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.914 Fit side-chains REVERT: A 20 ASP cc_start: 0.8368 (m-30) cc_final: 0.7955 (m-30) REVERT: B 217 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (ptt) REVERT: C 20 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7989 (mtpt) REVERT: C 58 GLU cc_start: 0.8780 (pm20) cc_final: 0.8278 (pm20) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 0.2166 time to fit residues: 40.2654 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106920 restraints weight = 11944.765| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.69 r_work: 0.3057 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8739 Z= 0.166 Angle : 0.515 7.523 11870 Z= 0.270 Chirality : 0.041 0.152 1356 Planarity : 0.003 0.030 1510 Dihedral : 4.463 71.496 1214 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 2.39 % Allowed : 15.11 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1106 helix: 2.24 (0.28), residues: 376 sheet: 0.76 (0.31), residues: 270 loop : -0.81 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.007 0.001 HIS R 94 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR D 178 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.008 Fit side-chains REVERT: A 20 ASP cc_start: 0.8398 (m-30) cc_final: 0.7976 (m-30) REVERT: B 217 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8244 (ptm) REVERT: C 20 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8003 (mtpt) REVERT: C 58 GLU cc_start: 0.8802 (pm20) cc_final: 0.8296 (pm20) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.2230 time to fit residues: 38.9152 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 130 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.0470 chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104713 restraints weight = 12092.884| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.56 r_work: 0.3025 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8739 Z= 0.241 Angle : 0.554 7.201 11870 Z= 0.294 Chirality : 0.043 0.185 1356 Planarity : 0.003 0.029 1510 Dihedral : 4.648 70.249 1214 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 2.61 % Allowed : 15.57 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1106 helix: 2.03 (0.28), residues: 382 sheet: 0.65 (0.31), residues: 270 loop : -1.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS R 94 PHE 0.013 0.002 PHE A 196 TYR 0.011 0.001 TYR D 178 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.876 Fit side-chains REVERT: A 20 ASP cc_start: 0.8422 (m-30) cc_final: 0.8136 (m-30) REVERT: B 217 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8081 (ptm) REVERT: C 20 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8078 (mtpt) REVERT: C 58 GLU cc_start: 0.8787 (pm20) cc_final: 0.8277 (pm20) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.2063 time to fit residues: 37.2879 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104258 restraints weight = 12231.683| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.35 r_work: 0.3031 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8739 Z= 0.268 Angle : 0.575 9.587 11870 Z= 0.303 Chirality : 0.043 0.179 1356 Planarity : 0.003 0.029 1510 Dihedral : 4.751 70.478 1214 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 2.73 % Allowed : 15.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1106 helix: 1.97 (0.28), residues: 380 sheet: 0.57 (0.31), residues: 270 loop : -1.07 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS R 94 PHE 0.013 0.002 PHE B 199 TYR 0.025 0.001 TYR R 57 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.047 Fit side-chains REVERT: A 20 ASP cc_start: 0.8386 (m-30) cc_final: 0.7928 (m-30) REVERT: B 217 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8150 (ptm) REVERT: C 20 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8030 (mtpt) REVERT: C 58 GLU cc_start: 0.8804 (pm20) cc_final: 0.8293 (pm20) outliers start: 24 outliers final: 20 residues processed: 125 average time/residue: 0.2237 time to fit residues: 38.3184 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104921 restraints weight = 12018.051| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.70 r_work: 0.3029 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8739 Z= 0.228 Angle : 0.553 8.927 11870 Z= 0.293 Chirality : 0.043 0.170 1356 Planarity : 0.003 0.031 1510 Dihedral : 4.682 71.420 1214 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1106 helix: 1.97 (0.28), residues: 381 sheet: 0.50 (0.31), residues: 274 loop : -1.02 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS R 94 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.001 TYR R 57 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.884 Fit side-chains REVERT: A 20 ASP cc_start: 0.8352 (m-30) cc_final: 0.7926 (m-30) REVERT: B 198 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8992 (mt) REVERT: B 217 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8046 (ptm) REVERT: C 20 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7923 (mtpt) REVERT: C 58 GLU cc_start: 0.8793 (pm20) cc_final: 0.8281 (pm20) outliers start: 22 outliers final: 18 residues processed: 126 average time/residue: 0.2100 time to fit residues: 36.0850 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 340 ASN D 130 GLN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107598 restraints weight = 12037.133| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.32 r_work: 0.3090 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8739 Z= 0.141 Angle : 0.505 8.936 11870 Z= 0.268 Chirality : 0.041 0.156 1356 Planarity : 0.003 0.033 1510 Dihedral : 4.466 73.599 1214 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 16.48 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1106 helix: 2.14 (0.28), residues: 377 sheet: 0.60 (0.32), residues: 268 loop : -0.80 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.007 0.001 HIS R 94 PHE 0.011 0.001 PHE D 80 TYR 0.022 0.001 TYR R 57 ARG 0.004 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.938 Fit side-chains REVERT: A 20 ASP cc_start: 0.8350 (m-30) cc_final: 0.7926 (m-30) REVERT: B 217 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8335 (ptt) REVERT: C 58 GLU cc_start: 0.8836 (pm20) cc_final: 0.8354 (pm20) outliers start: 17 outliers final: 15 residues processed: 127 average time/residue: 0.2185 time to fit residues: 37.9878 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.0000 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN R 72 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106599 restraints weight = 12112.370| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.77 r_work: 0.3095 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8739 Z= 0.111 Angle : 0.487 8.721 11870 Z= 0.254 Chirality : 0.040 0.143 1356 Planarity : 0.003 0.033 1510 Dihedral : 4.195 74.638 1214 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 17.05 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1106 helix: 2.13 (0.28), residues: 383 sheet: 0.73 (0.31), residues: 270 loop : -0.75 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.010 0.001 PHE D 80 TYR 0.021 0.001 TYR R 57 ARG 0.004 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5456.44 seconds wall clock time: 95 minutes 28.52 seconds (5728.52 seconds total)