Starting phenix.real_space_refine on Tue Jun 10 13:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7r_28908/06_2025/8f7r_28908.cif" } resolution = 3.28 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= 0.000 sd= 0.002 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 98 5.16 5 C 7615 2.51 5 N 1900 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11697 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Classifications: {'peptide': 4} Link IDs: {'PCIS': 1, 'TRANS': 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Modifications used: {'COO': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: Q Time building chain proxies: 8.04, per 1000 atoms: 0.69 Number of scatterers: 11697 At special positions: 0 Unit cell: (104.8, 108, 147.2, 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 98 16.00 O 2084 8.00 N 1900 7.00 C 7615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 48.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'R' and resid 68 through 98 Processing helix chain 'R' and resid 103 through 122 removed outlier: 3.915A pdb=" N THR R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.852A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.889A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.512A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.632A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 4.041A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.895A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.738A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (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 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.850A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.655A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.679A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.554A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.609A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 98 Processing helix chain 'M' and resid 103 through 122 removed outlier: 3.914A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.851A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.890A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.512A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.631A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 339 removed outlier: 4.041A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 339 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.535A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.657A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.876A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.680A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.799A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.985A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.476A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.726A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.586A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.805A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.602A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 653 hydrogen bonds defined for protein. 1890 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: 3.44 Time building geometry restraints manager: 3.30 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: 3509 1.34 - 1.46: 2327 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11977 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C5 CLR M 405 " pdb=" C6 CLR M 405 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C10 CLR M 401 " pdb=" C9 CLR M 401 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 11972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15627 1.94 - 3.88: 556 3.88 - 5.83: 92 5.83 - 7.77: 19 7.77 - 9.71: 5 Bond angle restraints: 16299 Sorted by residual: angle pdb=" N PRO A 288 " pdb=" CA PRO A 288 " pdb=" CB PRO A 288 " ideal model delta sigma weight residual 103.44 109.80 -6.36 1.12e+00 7.97e-01 3.22e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA PHE P 4 " pdb=" CB PHE P 4 " pdb=" CG PHE P 4 " ideal model delta sigma weight residual 113.80 116.70 -2.90 1.00e+00 1.00e+00 8.39e+00 angle pdb=" CA PHE Q 4 " pdb=" CB PHE Q 4 " pdb=" CG PHE Q 4 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.29e+00 ... (remaining 16294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.76: 6854 10.76 - 21.52: 596 21.52 - 32.28: 70 32.28 - 43.04: 33 43.04 - 53.81: 6 Dihedral angle restraints: 7559 sinusoidal: 3340 harmonic: 4219 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 7556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1706 0.092 - 0.183: 162 0.183 - 0.275: 15 0.275 - 0.367: 11 0.367 - 0.459: 9 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C14 CLR M 401 " pdb=" C13 CLR M 401 " pdb=" C15 CLR M 401 " pdb=" C8 CLR M 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C14 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C15 CLR R 405 " pdb=" C8 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1900 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 236 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 334 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO R 335 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 334 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO M 335 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 335 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 335 " 0.029 5.00e-02 4.00e+02 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2361 2.79 - 3.32: 10374 3.32 - 3.84: 19371 3.84 - 4.37: 21806 4.37 - 4.90: 39164 Nonbonded interactions: 93076 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.260 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.261 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.282 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.329 3.040 ... (remaining 93071 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 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 0.121 11982 Z= 0.270 Angle : 0.840 9.710 16305 Z= 0.443 Chirality : 0.065 0.459 1903 Planarity : 0.006 0.064 1962 Dihedral : 8.210 53.806 4822 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.71 (0.19), residues: 1421 helix: 0.10 (0.16), residues: 653 sheet: 0.12 (0.31), residues: 276 loop : -1.47 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 111 HIS 0.006 0.001 HIS E 35 PHE 0.022 0.002 PHE R 349 TYR 0.022 0.002 TYR R 108 ARG 0.008 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.15595 ( 653) hydrogen bonds : angle 6.58147 ( 1890) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.87917 ( 6) covalent geometry : bond 0.00425 (11977) covalent geometry : angle 0.83930 (16299) Misc. bond : bond 0.12118 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 SER cc_start: 0.7480 (t) cc_final: 0.7261 (m) REVERT: R 195 ILE cc_start: 0.8729 (mt) cc_final: 0.8447 (mm) REVERT: R 200 ILE cc_start: 0.8162 (tp) cc_final: 0.7721 (tp) REVERT: R 212 TYR cc_start: 0.6749 (m-80) cc_final: 0.6296 (m-80) REVERT: A 305 CYS cc_start: 0.6977 (t) cc_final: 0.6498 (t) REVERT: B 198 LEU cc_start: 0.7505 (pp) cc_final: 0.7156 (mt) REVERT: C 18 GLN cc_start: 0.6833 (tp40) cc_final: 0.6279 (mm110) REVERT: E 80 PHE cc_start: 0.6714 (m-80) cc_final: 0.6347 (m-10) REVERT: E 220 LEU cc_start: 0.8039 (tp) cc_final: 0.7827 (tt) REVERT: M 328 TYR cc_start: 0.7240 (m-80) cc_final: 0.6413 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2696 time to fit residues: 107.5088 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 91 HIS B 183 HIS B 266 HIS E 168 HIS E 184 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163554 restraints weight = 13364.670| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.27 r_work: 0.3792 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11982 Z= 0.151 Angle : 0.547 5.763 16305 Z= 0.288 Chirality : 0.040 0.142 1903 Planarity : 0.004 0.051 1962 Dihedral : 5.383 44.373 2215 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.19 % Allowed : 5.95 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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 (0.21), residues: 1421 helix: 1.84 (0.18), residues: 655 sheet: 0.32 (0.31), residues: 286 loop : -1.06 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.008 0.001 HIS B 225 PHE 0.020 0.002 PHE E 27 TYR 0.016 0.002 TYR E 191 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 653) hydrogen bonds : angle 4.87083 ( 1890) SS BOND : bond 0.00729 ( 3) SS BOND : angle 1.19764 ( 6) covalent geometry : bond 0.00329 (11977) covalent geometry : angle 0.54621 (16299) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8104 (tpp) cc_final: 0.7797 (tpt) REVERT: R 188 ILE cc_start: 0.8372 (mt) cc_final: 0.8155 (mp) REVERT: R 195 ILE cc_start: 0.8743 (mt) cc_final: 0.8095 (mm) REVERT: R 198 SER cc_start: 0.8378 (t) cc_final: 0.7890 (p) REVERT: R 212 TYR cc_start: 0.6934 (m-80) cc_final: 0.6298 (m-80) REVERT: A 197 LYS cc_start: 0.8514 (mttt) cc_final: 0.8100 (mmtm) REVERT: A 248 LYS cc_start: 0.7859 (mttp) cc_final: 0.7645 (mptt) REVERT: A 305 CYS cc_start: 0.8057 (t) cc_final: 0.7423 (t) REVERT: A 308 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: A 309 ASP cc_start: 0.6931 (m-30) cc_final: 0.6722 (m-30) REVERT: B 172 GLU cc_start: 0.7113 (tp30) cc_final: 0.6665 (tm-30) REVERT: C 18 GLN cc_start: 0.6955 (tp40) cc_final: 0.6367 (mm110) REVERT: E 55 SER cc_start: 0.7482 (m) cc_final: 0.6921 (p) REVERT: E 80 PHE cc_start: 0.6811 (m-80) cc_final: 0.6263 (m-10) REVERT: E 220 LEU cc_start: 0.8259 (tp) cc_final: 0.8002 (tt) REVERT: M 196 LEU cc_start: 0.7269 (mt) cc_final: 0.6976 (mt) REVERT: M 234 LEU cc_start: 0.8388 (tp) cc_final: 0.7933 (tp) REVERT: M 245 MET cc_start: 0.6279 (mmt) cc_final: 0.5747 (ttm) outliers start: 15 outliers final: 10 residues processed: 246 average time/residue: 0.3008 time to fit residues: 103.6268 Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 101 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS M 193 ASN M 299 HIS M 321 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.179133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143153 restraints weight = 13549.813| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.96 r_work: 0.3580 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11982 Z= 0.234 Angle : 0.638 5.847 16305 Z= 0.335 Chirality : 0.044 0.154 1903 Planarity : 0.005 0.047 1962 Dihedral : 5.688 35.783 2215 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.62 % Allowed : 8.72 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 0.93 (0.22), residues: 1421 helix: 1.84 (0.19), residues: 659 sheet: 0.19 (0.31), residues: 297 loop : -0.84 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.011 0.002 HIS B 54 PHE 0.019 0.003 PHE E 27 TYR 0.025 0.002 TYR R 301 ARG 0.010 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 653) hydrogen bonds : angle 4.89770 ( 1890) SS BOND : bond 0.00231 ( 3) SS BOND : angle 1.05956 ( 6) covalent geometry : bond 0.00551 (11977) covalent geometry : angle 0.63825 (16299) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8401 (tpp) cc_final: 0.8011 (tpt) REVERT: R 102 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7066 (mmtm) REVERT: R 195 ILE cc_start: 0.8753 (mt) cc_final: 0.8087 (mm) REVERT: R 198 SER cc_start: 0.8794 (t) cc_final: 0.8294 (p) REVERT: R 211 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7724 (mttm) REVERT: R 212 TYR cc_start: 0.6809 (m-80) cc_final: 0.6176 (m-80) REVERT: R 283 MET cc_start: 0.7827 (tpp) cc_final: 0.6939 (mtt) REVERT: R 340 PHE cc_start: 0.7739 (m-10) cc_final: 0.7380 (m-10) REVERT: A 21 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7527 (ttm110) REVERT: A 197 LYS cc_start: 0.8657 (mttt) cc_final: 0.8299 (mttm) REVERT: A 244 HIS cc_start: 0.8225 (m90) cc_final: 0.7933 (m-70) REVERT: A 305 CYS cc_start: 0.8185 (t) cc_final: 0.7858 (t) REVERT: A 308 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 82 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: B 172 GLU cc_start: 0.7761 (tp30) cc_final: 0.7368 (tm-30) REVERT: B 239 ASN cc_start: 0.7811 (m-40) cc_final: 0.6986 (p0) REVERT: E 38 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7413 (ptp90) REVERT: E 141 MET cc_start: 0.7603 (mmm) cc_final: 0.7198 (mmm) REVERT: E 161 ARG cc_start: 0.7114 (mmm160) cc_final: 0.6550 (mpp80) REVERT: E 193 MET cc_start: 0.6577 (mmm) cc_final: 0.5993 (ttp) REVERT: M 124 PRO cc_start: 0.6657 (Cg_exo) cc_final: 0.6378 (Cg_endo) REVERT: M 126 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6351 (tt0) REVERT: M 332 CYS cc_start: 0.6743 (t) cc_final: 0.6179 (p) outliers start: 33 outliers final: 22 residues processed: 241 average time/residue: 0.3259 time to fit residues: 111.0862 Evaluate side-chains 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 126 GLN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 131 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** M 106 ASN ** 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 = 0.4150 r_free = 0.4150 target = 0.183600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150014 restraints weight = 13311.182| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.98 r_work: 0.3630 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11982 Z= 0.120 Angle : 0.512 7.047 16305 Z= 0.266 Chirality : 0.039 0.140 1903 Planarity : 0.004 0.044 1962 Dihedral : 5.061 31.907 2215 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.38 % Allowed : 11.90 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.40 (0.22), residues: 1421 helix: 2.27 (0.19), residues: 660 sheet: 0.34 (0.31), residues: 290 loop : -0.60 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.001 PHE E 27 TYR 0.015 0.001 TYR E 191 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 653) hydrogen bonds : angle 4.57788 ( 1890) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.70940 ( 6) covalent geometry : bond 0.00268 (11977) covalent geometry : angle 0.51241 (16299) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8368 (tpp) cc_final: 0.7986 (tpt) REVERT: R 195 ILE cc_start: 0.8701 (mt) cc_final: 0.7981 (mm) REVERT: R 198 SER cc_start: 0.8772 (t) cc_final: 0.8220 (p) REVERT: R 212 TYR cc_start: 0.6746 (m-80) cc_final: 0.6050 (m-80) REVERT: R 283 MET cc_start: 0.7716 (tpp) cc_final: 0.6910 (mtt) REVERT: R 340 PHE cc_start: 0.7656 (m-10) cc_final: 0.6137 (t80) REVERT: A 21 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7631 (ttm110) REVERT: A 197 LYS cc_start: 0.8662 (mttt) cc_final: 0.8327 (mttm) REVERT: A 244 HIS cc_start: 0.8169 (m90) cc_final: 0.7891 (m-70) REVERT: A 298 GLU cc_start: 0.5928 (tt0) cc_final: 0.5393 (pt0) REVERT: A 305 CYS cc_start: 0.8191 (t) cc_final: 0.7895 (t) REVERT: A 308 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: B 172 GLU cc_start: 0.7670 (tp30) cc_final: 0.7315 (tm-30) REVERT: B 239 ASN cc_start: 0.7967 (m-40) cc_final: 0.7273 (p0) REVERT: E 38 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7392 (ptp90) REVERT: E 141 MET cc_start: 0.7612 (mmm) cc_final: 0.7149 (mmm) REVERT: E 161 ARG cc_start: 0.7138 (mmm160) cc_final: 0.6616 (mpp80) REVERT: E 193 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5934 (ttp) REVERT: M 92 MET cc_start: 0.6327 (mmt) cc_final: 0.5751 (mmt) REVERT: M 124 PRO cc_start: 0.6577 (Cg_exo) cc_final: 0.6328 (Cg_endo) REVERT: M 231 GLU cc_start: 0.7555 (tt0) cc_final: 0.7314 (tp30) outliers start: 30 outliers final: 16 residues processed: 209 average time/residue: 0.2762 time to fit residues: 80.6168 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 176 GLN E 168 HIS ** M 106 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.185633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152074 restraints weight = 13311.807| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.01 r_work: 0.3658 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11982 Z= 0.103 Angle : 0.479 5.596 16305 Z= 0.249 Chirality : 0.039 0.139 1903 Planarity : 0.004 0.042 1962 Dihedral : 4.823 31.158 2215 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.46 % Allowed : 11.90 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.74 (0.22), residues: 1421 helix: 2.57 (0.20), residues: 660 sheet: 0.48 (0.31), residues: 290 loop : -0.47 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS E 168 PHE 0.029 0.001 PHE A 334 TYR 0.014 0.001 TYR E 191 ARG 0.006 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 653) hydrogen bonds : angle 4.36086 ( 1890) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.78968 ( 6) covalent geometry : bond 0.00226 (11977) covalent geometry : angle 0.47877 (16299) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8340 (tpp) cc_final: 0.7990 (tpt) REVERT: R 195 ILE cc_start: 0.8753 (mt) cc_final: 0.8059 (mm) REVERT: R 198 SER cc_start: 0.8764 (t) cc_final: 0.8216 (p) REVERT: R 212 TYR cc_start: 0.6657 (m-80) cc_final: 0.5954 (m-80) REVERT: R 283 MET cc_start: 0.7644 (tpp) cc_final: 0.6910 (mtt) REVERT: R 340 PHE cc_start: 0.7489 (m-10) cc_final: 0.6104 (t80) REVERT: A 21 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7675 (ttm110) REVERT: A 197 LYS cc_start: 0.8617 (mttt) cc_final: 0.8369 (mttm) REVERT: A 244 HIS cc_start: 0.8139 (m90) cc_final: 0.7876 (m-70) REVERT: A 305 CYS cc_start: 0.8185 (t) cc_final: 0.7957 (t) REVERT: B 82 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: B 172 GLU cc_start: 0.7572 (tp30) cc_final: 0.7262 (tm-30) REVERT: E 38 ARG cc_start: 0.7645 (ptp90) cc_final: 0.7427 (ptp90) REVERT: E 55 SER cc_start: 0.7755 (m) cc_final: 0.7199 (p) REVERT: E 73 ASP cc_start: 0.5510 (OUTLIER) cc_final: 0.4958 (t70) REVERT: E 141 MET cc_start: 0.7582 (mmm) cc_final: 0.7059 (mmm) REVERT: E 161 ARG cc_start: 0.7096 (mmm160) cc_final: 0.6606 (mpp80) REVERT: E 193 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5803 (ttp) REVERT: M 92 MET cc_start: 0.6431 (mmt) cc_final: 0.5759 (mmt) REVERT: M 124 PRO cc_start: 0.6603 (Cg_exo) cc_final: 0.6334 (Cg_endo) REVERT: M 231 GLU cc_start: 0.7621 (tt0) cc_final: 0.7377 (tp30) outliers start: 31 outliers final: 18 residues processed: 217 average time/residue: 0.2911 time to fit residues: 89.1933 Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 126 GLN Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 54 optimal weight: 8.9990 chunk 101 optimal weight: 0.0670 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 176 GLN E 82 GLN E 168 HIS ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146240 restraints weight = 13536.772| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.86 r_work: 0.3593 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11982 Z= 0.161 Angle : 0.529 6.663 16305 Z= 0.274 Chirality : 0.040 0.136 1903 Planarity : 0.004 0.045 1962 Dihedral : 5.032 32.019 2215 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.62 % Allowed : 13.01 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.56 (0.22), residues: 1421 helix: 2.42 (0.19), residues: 659 sheet: 0.44 (0.31), residues: 292 loop : -0.59 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 3 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE B 278 TYR 0.014 0.001 TYR R 301 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 653) hydrogen bonds : angle 4.48887 ( 1890) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.89148 ( 6) covalent geometry : bond 0.00377 (11977) covalent geometry : angle 0.52865 (16299) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8313 (tpp) cc_final: 0.7956 (tpt) REVERT: R 195 ILE cc_start: 0.8746 (mt) cc_final: 0.8052 (mm) REVERT: R 198 SER cc_start: 0.8790 (t) cc_final: 0.8255 (p) REVERT: R 212 TYR cc_start: 0.6609 (m-80) cc_final: 0.5932 (m-80) REVERT: R 283 MET cc_start: 0.7585 (tpp) cc_final: 0.6907 (mtt) REVERT: A 197 LYS cc_start: 0.8663 (mttt) cc_final: 0.8363 (mttm) REVERT: A 305 CYS cc_start: 0.8178 (t) cc_final: 0.7928 (t) REVERT: A 308 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: B 82 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: B 172 GLU cc_start: 0.7481 (tp30) cc_final: 0.7260 (tm-30) REVERT: E 73 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5068 (t70) REVERT: E 141 MET cc_start: 0.7647 (mmm) cc_final: 0.7089 (mmm) REVERT: E 161 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6565 (mpp80) REVERT: E 181 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: E 187 GLN cc_start: 0.8593 (pt0) cc_final: 0.8315 (pt0) REVERT: E 193 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5963 (ttp) REVERT: M 92 MET cc_start: 0.6507 (mmt) cc_final: 0.5825 (mmt) REVERT: M 124 PRO cc_start: 0.6577 (Cg_exo) cc_final: 0.6302 (Cg_endo) REVERT: M 231 GLU cc_start: 0.7552 (tt0) cc_final: 0.7302 (tp30) outliers start: 33 outliers final: 23 residues processed: 216 average time/residue: 0.2510 time to fit residues: 75.8585 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN A 306 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** M 106 ASN ** 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 = 0.4130 r_free = 0.4130 target = 0.181578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148544 restraints weight = 13582.563| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.99 r_work: 0.3609 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11982 Z= 0.122 Angle : 0.504 6.233 16305 Z= 0.261 Chirality : 0.039 0.140 1903 Planarity : 0.004 0.042 1962 Dihedral : 4.922 31.671 2215 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.70 % Allowed : 13.48 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.68 (0.22), residues: 1421 helix: 2.51 (0.20), residues: 660 sheet: 0.56 (0.31), residues: 288 loop : -0.56 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.014 0.001 PHE E 27 TYR 0.013 0.001 TYR E 191 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 653) hydrogen bonds : angle 4.39245 ( 1890) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.71172 ( 6) covalent geometry : bond 0.00279 (11977) covalent geometry : angle 0.50347 (16299) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8284 (tpp) cc_final: 0.7902 (tpt) REVERT: R 195 ILE cc_start: 0.8735 (mt) cc_final: 0.8027 (mm) REVERT: R 198 SER cc_start: 0.8774 (t) cc_final: 0.8224 (p) REVERT: R 212 TYR cc_start: 0.6587 (m-80) cc_final: 0.5913 (m-80) REVERT: R 283 MET cc_start: 0.7535 (tpp) cc_final: 0.6931 (mtt) REVERT: R 340 PHE cc_start: 0.7659 (m-10) cc_final: 0.7257 (m-10) REVERT: A 197 LYS cc_start: 0.8648 (mttt) cc_final: 0.8371 (mttm) REVERT: A 305 CYS cc_start: 0.8155 (t) cc_final: 0.7913 (t) REVERT: A 308 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: B 82 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: B 172 GLU cc_start: 0.7589 (tp30) cc_final: 0.7327 (tm-30) REVERT: E 73 ASP cc_start: 0.5663 (OUTLIER) cc_final: 0.5007 (t70) REVERT: E 141 MET cc_start: 0.7623 (mmm) cc_final: 0.6978 (mmm) REVERT: E 161 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6575 (mpp80) REVERT: E 193 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5974 (ttp) REVERT: M 124 PRO cc_start: 0.6532 (Cg_exo) cc_final: 0.6264 (Cg_endo) REVERT: M 231 GLU cc_start: 0.7544 (tt0) cc_final: 0.7284 (tp30) outliers start: 34 outliers final: 24 residues processed: 203 average time/residue: 0.2426 time to fit residues: 70.2967 Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN E 187 GLN ** M 88 ASN ** 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 = 0.4039 r_free = 0.4039 target = 0.172509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138551 restraints weight = 13642.790| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.94 r_work: 0.3502 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11982 Z= 0.262 Angle : 0.634 6.361 16305 Z= 0.331 Chirality : 0.044 0.160 1903 Planarity : 0.004 0.046 1962 Dihedral : 5.740 41.133 2215 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.49 % Allowed : 12.77 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.16 (0.22), residues: 1421 helix: 2.01 (0.19), residues: 659 sheet: 0.31 (0.31), residues: 289 loop : -0.68 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 82 HIS 0.006 0.002 HIS B 62 PHE 0.019 0.002 PHE B 292 TYR 0.024 0.002 TYR R 301 ARG 0.007 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 653) hydrogen bonds : angle 4.79587 ( 1890) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.99033 ( 6) covalent geometry : bond 0.00623 (11977) covalent geometry : angle 0.63375 (16299) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8415 (tpp) cc_final: 0.8072 (tpt) REVERT: R 195 ILE cc_start: 0.8762 (mt) cc_final: 0.8075 (mm) REVERT: R 198 SER cc_start: 0.8875 (t) cc_final: 0.8343 (p) REVERT: R 212 TYR cc_start: 0.6549 (m-80) cc_final: 0.5921 (m-80) REVERT: R 283 MET cc_start: 0.7849 (tpp) cc_final: 0.7146 (mtt) REVERT: R 340 PHE cc_start: 0.7959 (m-10) cc_final: 0.7634 (m-10) REVERT: A 197 LYS cc_start: 0.8690 (mttt) cc_final: 0.8404 (mttm) REVERT: A 298 GLU cc_start: 0.5691 (tt0) cc_final: 0.5314 (pt0) REVERT: A 305 CYS cc_start: 0.8198 (t) cc_final: 0.7930 (t) REVERT: A 308 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 82 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: B 134 ARG cc_start: 0.7376 (ptt-90) cc_final: 0.6665 (ttt180) REVERT: B 239 ASN cc_start: 0.7951 (m-40) cc_final: 0.7175 (p0) REVERT: E 73 ASP cc_start: 0.6095 (OUTLIER) cc_final: 0.5353 (t70) REVERT: E 161 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6668 (mpp80) REVERT: E 193 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6250 (ttp) REVERT: M 92 MET cc_start: 0.6486 (mmt) cc_final: 0.5828 (mmt) REVERT: M 124 PRO cc_start: 0.6497 (Cg_exo) cc_final: 0.6257 (Cg_endo) REVERT: M 231 GLU cc_start: 0.7575 (tt0) cc_final: 0.7337 (tp30) outliers start: 44 outliers final: 30 residues processed: 217 average time/residue: 0.2547 time to fit residues: 77.3766 Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 317 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 214 GLN R 330 ASN A 213 HIS A 269 ASN A 306 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.177117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143391 restraints weight = 13569.109| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.90 r_work: 0.3570 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11982 Z= 0.141 Angle : 0.540 9.003 16305 Z= 0.279 Chirality : 0.040 0.131 1903 Planarity : 0.004 0.044 1962 Dihedral : 5.331 40.474 2215 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.62 % Allowed : 14.20 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.38 (0.22), residues: 1421 helix: 2.25 (0.20), residues: 661 sheet: 0.39 (0.31), residues: 287 loop : -0.68 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.001 PHE A 307 TYR 0.017 0.001 TYR B 59 ARG 0.008 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 653) hydrogen bonds : angle 4.58615 ( 1890) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.80296 ( 6) covalent geometry : bond 0.00327 (11977) covalent geometry : angle 0.53989 (16299) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8343 (tpp) cc_final: 0.7955 (tpt) REVERT: R 198 SER cc_start: 0.8822 (t) cc_final: 0.8262 (p) REVERT: R 212 TYR cc_start: 0.6551 (m-80) cc_final: 0.5894 (m-80) REVERT: R 283 MET cc_start: 0.7657 (tpp) cc_final: 0.7024 (mtt) REVERT: A 197 LYS cc_start: 0.8703 (mttt) cc_final: 0.8467 (mttm) REVERT: A 298 GLU cc_start: 0.5607 (tt0) cc_final: 0.5252 (pt0) REVERT: A 305 CYS cc_start: 0.8152 (t) cc_final: 0.7895 (t) REVERT: A 308 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: B 82 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: B 134 ARG cc_start: 0.7073 (ptt-90) cc_final: 0.6496 (ttt180) REVERT: B 239 ASN cc_start: 0.8000 (m-40) cc_final: 0.7345 (p0) REVERT: B 292 PHE cc_start: 0.7630 (m-80) cc_final: 0.7384 (m-80) REVERT: E 141 MET cc_start: 0.7584 (mmm) cc_final: 0.6707 (mmm) REVERT: E 161 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6580 (mpp80) REVERT: E 193 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.6203 (ttp) REVERT: M 124 PRO cc_start: 0.6493 (Cg_exo) cc_final: 0.6267 (Cg_endo) REVERT: M 220 THR cc_start: 0.7872 (t) cc_final: 0.7597 (p) REVERT: M 231 GLU cc_start: 0.7493 (tt0) cc_final: 0.7275 (tp30) REVERT: M 248 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7998 (tp) outliers start: 33 outliers final: 24 residues processed: 207 average time/residue: 0.2418 time to fit residues: 71.2351 Evaluate side-chains 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN E 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.175089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140903 restraints weight = 13518.139| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.92 r_work: 0.3543 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11982 Z= 0.204 Angle : 0.583 9.174 16305 Z= 0.301 Chirality : 0.042 0.221 1903 Planarity : 0.004 0.044 1962 Dihedral : 5.433 43.142 2215 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.46 % Allowed : 14.83 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.26 (0.22), residues: 1421 helix: 2.14 (0.20), residues: 661 sheet: 0.35 (0.31), residues: 287 loop : -0.71 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.005 0.001 HIS B 183 PHE 0.022 0.002 PHE B 292 TYR 0.018 0.002 TYR R 301 ARG 0.008 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 653) hydrogen bonds : angle 4.63124 ( 1890) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.98111 ( 6) covalent geometry : bond 0.00484 (11977) covalent geometry : angle 0.58266 (16299) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.8379 (tpp) cc_final: 0.8012 (tpt) REVERT: R 198 SER cc_start: 0.8834 (t) cc_final: 0.8280 (p) REVERT: R 212 TYR cc_start: 0.6610 (m-80) cc_final: 0.5948 (m-80) REVERT: R 283 MET cc_start: 0.7718 (tpp) cc_final: 0.7067 (mtt) REVERT: A 197 LYS cc_start: 0.8725 (mttt) cc_final: 0.8491 (mttm) REVERT: A 298 GLU cc_start: 0.5581 (tt0) cc_final: 0.5227 (pt0) REVERT: A 305 CYS cc_start: 0.8160 (t) cc_final: 0.7889 (t) REVERT: A 308 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: B 82 TRP cc_start: 0.7664 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: B 134 ARG cc_start: 0.7175 (ptt-90) cc_final: 0.6588 (ttt180) REVERT: B 239 ASN cc_start: 0.7959 (m-40) cc_final: 0.7322 (p0) REVERT: B 292 PHE cc_start: 0.7714 (m-80) cc_final: 0.7413 (m-80) REVERT: E 38 ARG cc_start: 0.7855 (ptp90) cc_final: 0.7490 (ptp90) REVERT: E 141 MET cc_start: 0.7585 (mmm) cc_final: 0.6749 (mmm) REVERT: E 161 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6594 (mpp80) REVERT: E 193 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6209 (ttp) REVERT: M 124 PRO cc_start: 0.6515 (Cg_exo) cc_final: 0.6288 (Cg_endo) REVERT: M 220 THR cc_start: 0.7923 (t) cc_final: 0.7639 (p) REVERT: M 231 GLU cc_start: 0.7511 (tt0) cc_final: 0.7287 (tp30) REVERT: M 248 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8036 (tp) outliers start: 31 outliers final: 24 residues processed: 207 average time/residue: 0.2407 time to fit residues: 71.2025 Evaluate side-chains 211 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 101 MET Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN A 333 GLN B 75 GLN B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142490 restraints weight = 13457.490| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.97 r_work: 0.3565 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11982 Z= 0.148 Angle : 0.542 10.169 16305 Z= 0.280 Chirality : 0.040 0.179 1903 Planarity : 0.004 0.043 1962 Dihedral : 5.309 45.854 2215 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.62 % Allowed : 14.51 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.31 (0.22), residues: 1421 helix: 2.19 (0.20), residues: 667 sheet: 0.30 (0.31), residues: 287 loop : -0.69 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.002 PHE B 292 TYR 0.014 0.001 TYR M 108 ARG 0.008 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 653) hydrogen bonds : angle 4.53741 ( 1890) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.82875 ( 6) covalent geometry : bond 0.00347 (11977) covalent geometry : angle 0.54176 (16299) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7241.76 seconds wall clock time: 127 minutes 22.81 seconds (7642.81 seconds total)