Starting phenix.real_space_refine on Thu Jul 2 14:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0q_34414/07_2026/8h0q_34414.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 58 5.16 5 C 5730 2.51 5 N 1520 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2356 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1705 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2576 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1753 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 401 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8949 At special positions: 0 Unit cell: (122.4, 92.8, 128, 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 58 16.00 O 1641 8.00 N 1520 7.00 C 5730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 42 through 68 Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.558A pdb=" N LEU R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE R 79 " --> pdb=" O PRO R 75 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 111 through 142 removed outlier: 3.643A pdb=" N LEU R 115 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE R 116 " --> pdb=" O GLY R 112 " (cutoff:3.500A) Proline residue: R 117 - end of helix removed outlier: 3.730A pdb=" N GLN R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 178 removed outlier: 3.589A pdb=" N CYS R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 174 - end of helix Processing helix chain 'R' and resid 204 through 219 removed outlier: 3.843A pdb=" N LYS R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 241 Processing helix chain 'R' and resid 249 through 290 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 297 through 318 removed outlier: 3.921A pdb=" N SER R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 326 Processing helix chain 'R' and resid 329 through 339 removed outlier: 4.046A pdb=" N LEU R 337 " --> pdb=" O PHE R 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.555A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.563A pdb=" N GLN A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.824A pdb=" N ARG A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.580A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.645A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 58 Processing sheet with id=AA1, first strand: chain 'R' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 196 removed outlier: 6.269A pdb=" N LEU A 40 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 42 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL A 206 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A 44 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 225 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 269 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N HIS A 327 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 271 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.839A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 56 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 7.052A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.981A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 119 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.933A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.826A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.635A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.026A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 292 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.690A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 82 " --> pdb=" O ARG E 17 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.931A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.811A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 3 1.06 - 1.26: 1436 1.26 - 1.46: 2822 1.46 - 1.65: 4789 1.65 - 1.85: 95 Bond restraints: 9145 Sorted by residual: bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 0.868 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C13 CLR R 402 " pdb=" C17 CLR R 402 " ideal model delta sigma weight residual 1.550 0.869 0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C13 CLR R 403 " pdb=" C17 CLR R 403 " ideal model delta sigma weight residual 1.550 0.870 0.680 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C15 CLR R 403 " pdb=" C16 CLR R 403 " ideal model delta sigma weight residual 1.541 1.166 0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.167 0.374 2.00e-02 2.50e+03 3.50e+02 ... (remaining 9140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 12305 2.44 - 4.88: 87 4.88 - 7.31: 7 7.31 - 9.75: 3 9.75 - 12.19: 9 Bond angle restraints: 12411 Sorted by residual: angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 112.92 12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C4 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 120.33 108.32 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " pdb=" C7 CLR R 403 " ideal model delta sigma weight residual 125.11 113.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 113.22 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" C4 CLR R 403 " pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 120.33 108.45 11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 12406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.45: 5087 11.45 - 22.90: 218 22.90 - 34.35: 70 34.35 - 45.80: 20 45.80 - 57.26: 7 Dihedral angle restraints: 5402 sinusoidal: 2099 harmonic: 3303 Sorted by residual: dihedral pdb=" CA CYS E 95 " pdb=" C CYS E 95 " pdb=" N VAL E 96 " pdb=" CA VAL E 96 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" N ARG B 288 " pdb=" CA ARG B 288 " pdb=" CB ARG B 288 " pdb=" CG ARG B 288 " ideal model delta sinusoidal sigma weight residual -60.00 -117.26 57.26 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA LYS R 331 " pdb=" CB LYS R 331 " pdb=" CG LYS R 331 " pdb=" CD LYS R 331 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 5399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 1414 0.328 - 0.656: 3 0.656 - 0.985: 0 0.985 - 1.313: 0 1.313 - 1.641: 3 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -1.29 -1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -1.29 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -1.30 -1.64 2.00e-01 2.50e+01 6.70e+01 ... (remaining 1417 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 95 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C CYS E 95 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS E 95 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL E 96 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 125 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C GLY R 125 " 0.021 2.00e-02 2.50e+03 pdb=" O GLY R 125 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL R 126 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 126 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL R 126 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL R 126 " 0.008 2.00e-02 2.50e+03 pdb=" N SER R 127 " 0.007 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2030 2.79 - 3.32: 8363 3.32 - 3.84: 14483 3.84 - 4.37: 16305 4.37 - 4.90: 28841 Nonbonded interactions: 70022 Sorted by model distance: nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.260 3.040 nonbonded pdb=" OG SER R 258 " pdb=" O VAL A 359 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR R 199 " pdb=" OH TYR R 284 " model vdw 2.307 3.040 nonbonded pdb=" O ARG A 338 " pdb=" ND2 ASN A 342 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR R 296 " pdb=" OD1 ASN L 19 " model vdw 2.340 3.040 ... (remaining 70017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.019 0.682 9147 Z= 0.932 Angle : 0.589 12.188 12415 Z= 0.281 Chirality : 0.090 1.641 1420 Planarity : 0.003 0.041 1551 Dihedral : 7.887 57.256 3258 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.62 % Allowed : 4.89 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.23), residues: 1110 helix: 0.32 (0.25), residues: 375 sheet: -1.81 (0.28), residues: 254 loop : -2.29 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.005 0.000 TYR E 101 PHE 0.006 0.001 PHE R 118 TRP 0.005 0.001 TRP B 174 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.01862 / 0.93 ( 9145) covalent geometry : angle 0.58930 / 0.28 (12411) SS BOND : bond 0.00133 / 0.07 ( 2) SS BOND : angle 0.45896 / 0.25 ( 4) hydrogen bonds : bond 0.13930 / 9.78 ( 416) hydrogen bonds : angle 5.09501 / 3.75 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 412 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8393 (mt) cc_final: 0.8147 (mt) REVERT: R 205 LEU cc_start: 0.9178 (tp) cc_final: 0.8972 (tt) REVERT: A 34 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7776 (tp40) REVERT: A 58 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 315 ASP cc_start: 0.7476 (t70) cc_final: 0.7255 (t0) REVERT: B 17 GLU cc_start: 0.9244 (tp30) cc_final: 0.9010 (tp30) REVERT: B 83 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7471 (mmtm) REVERT: B 193 MET cc_start: 0.8421 (mmm) cc_final: 0.8084 (mmt) REVERT: B 203 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 223 CYS cc_start: 0.7283 (p) cc_final: 0.6985 (t) REVERT: B 285 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8081 (ttmm) REVERT: E 13 PRO cc_start: 0.8924 (Cg_endo) cc_final: 0.8217 (Cg_exo) REVERT: E 45 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7805 (mt-10) REVERT: E 52 SER cc_start: 0.8375 (p) cc_final: 0.7684 (t) REVERT: E 67 PHE cc_start: 0.7555 (m-80) cc_final: 0.7311 (m-80) REVERT: E 90 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8368 (t) REVERT: E 206 SER cc_start: 0.8344 (t) cc_final: 0.7979 (p) REVERT: G 13 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8394 (mtpp) REVERT: G 15 VAL cc_start: 0.9560 (p) cc_final: 0.9286 (p) REVERT: G 31 LYS cc_start: 0.9279 (tttp) cc_final: 0.8638 (tptm) outliers start: 6 outliers final: 2 residues processed: 418 average time/residue: 0.1161 time to fit residues: 62.9174 Evaluate side-chains 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 341 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 357 ASN B 59 HIS B 67 HIS B 93 ASN B 316 HIS ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 43 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.120432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092684 restraints weight = 17055.901| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.09 r_work: 0.3182 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9147 Z= 0.320 Angle : 0.776 6.817 12415 Z= 0.401 Chirality : 0.048 0.175 1420 Planarity : 0.005 0.047 1551 Dihedral : 5.161 51.285 1257 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.20 % Allowed : 15.49 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1110 helix: 1.21 (0.26), residues: 378 sheet: -1.57 (0.28), residues: 271 loop : -1.66 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.019 0.002 TYR R 199 PHE 0.020 0.002 PHE R 275 TRP 0.021 0.002 TRP B 302 HIS 0.009 0.002 HIS R 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.32 ( 9145) covalent geometry : angle 0.77497 / 0.40 (12411) SS BOND : bond 0.01643 / 0.86 ( 2) SS BOND : angle 1.94372 / 0.98 ( 4) hydrogen bonds : bond 0.04222 / 2.89 ( 416) hydrogen bonds : angle 4.48561 / 3.28 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8132 (tt) REVERT: R 163 PHE cc_start: 0.7699 (t80) cc_final: 0.7385 (t80) REVERT: R 205 LEU cc_start: 0.9295 (tp) cc_final: 0.9023 (tt) REVERT: R 239 GLN cc_start: 0.8532 (tp40) cc_final: 0.8214 (tm-30) REVERT: R 242 TYR cc_start: 0.8135 (m-10) cc_final: 0.7917 (m-10) REVERT: R 286 TYR cc_start: 0.8400 (t80) cc_final: 0.7926 (t80) REVERT: L 26 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6886 (pp) REVERT: A 26 GLU cc_start: 0.8383 (tp30) cc_final: 0.7953 (tp30) REVERT: A 28 GLN cc_start: 0.8594 (tp40) cc_final: 0.8355 (tp40) REVERT: A 34 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7969 (mm-40) REVERT: A 198 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9082 (mtmm) REVERT: A 253 ASN cc_start: 0.9356 (OUTLIER) cc_final: 0.8614 (m110) REVERT: B 135 GLU cc_start: 0.8852 (mp0) cc_final: 0.8636 (mp0) REVERT: B 203 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8790 (pp) REVERT: B 220 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: B 285 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8199 (ttmm) REVERT: B 302 TRP cc_start: 0.9178 (m100) cc_final: 0.8637 (m-10) REVERT: B 344 TRP cc_start: 0.8922 (m100) cc_final: 0.8621 (m-10) REVERT: E 2 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7735 (mm-40) REVERT: E 42 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8928 (mmmm) REVERT: E 45 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8335 (mt-10) REVERT: E 72 ASP cc_start: 0.7448 (t70) cc_final: 0.6789 (p0) REVERT: E 90 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8428 (t) REVERT: E 138 ILE cc_start: 0.8383 (mm) cc_final: 0.8085 (mm) REVERT: E 165 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7594 (pp) REVERT: E 192 MET cc_start: 0.7358 (ptm) cc_final: 0.7037 (ptm) REVERT: E 202 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6859 (mtm110) REVERT: E 223 ASP cc_start: 0.9082 (p0) cc_final: 0.8651 (p0) REVERT: G 12 ARG cc_start: 0.8945 (ptp-170) cc_final: 0.8515 (ptp90) REVERT: G 31 LYS cc_start: 0.9207 (tttp) cc_final: 0.8910 (tptm) REVERT: G 35 ASP cc_start: 0.8822 (m-30) cc_final: 0.8412 (m-30) outliers start: 50 outliers final: 23 residues processed: 270 average time/residue: 0.0890 time to fit residues: 33.4933 Evaluate side-chains 217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 GLN L 20 HIS ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN B 59 HIS B 93 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN G 43 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.119560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089404 restraints weight = 17127.696| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.99 r_work: 0.3210 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9147 Z= 0.136 Angle : 0.580 8.468 12415 Z= 0.297 Chirality : 0.043 0.171 1420 Planarity : 0.004 0.040 1551 Dihedral : 4.599 45.385 1256 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.99 % Allowed : 16.84 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.26), residues: 1110 helix: 1.65 (0.27), residues: 387 sheet: -1.61 (0.28), residues: 270 loop : -1.22 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.013 0.001 TYR A 235 PHE 0.015 0.001 PHE A 228 TRP 0.036 0.001 TRP L 21 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9145) covalent geometry : angle 0.57827 / 0.30 (12411) SS BOND : bond 0.00861 / 0.45 ( 2) SS BOND : angle 2.57026 / 1.44 ( 4) hydrogen bonds : bond 0.03373 / 2.34 ( 416) hydrogen bonds : angle 3.96321 / 2.88 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8215 (tt) REVERT: R 90 LEU cc_start: 0.8635 (mt) cc_final: 0.8427 (mt) REVERT: R 205 LEU cc_start: 0.9250 (tp) cc_final: 0.8990 (tt) REVERT: R 212 MET cc_start: 0.8305 (tpp) cc_final: 0.6964 (ttt) REVERT: R 239 GLN cc_start: 0.8404 (tp40) cc_final: 0.8077 (tm-30) REVERT: R 286 TYR cc_start: 0.8292 (t80) cc_final: 0.7880 (t80) REVERT: A 26 GLU cc_start: 0.8363 (tp30) cc_final: 0.7923 (tp30) REVERT: A 28 GLN cc_start: 0.8559 (tp40) cc_final: 0.8311 (tp40) REVERT: A 193 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: A 198 LYS cc_start: 0.9310 (mmtt) cc_final: 0.9042 (mtmm) REVERT: B 135 GLU cc_start: 0.8777 (mp0) cc_final: 0.8485 (mp0) REVERT: B 203 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 220 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: B 302 TRP cc_start: 0.9089 (m100) cc_final: 0.8570 (m-10) REVERT: B 344 TRP cc_start: 0.8892 (m100) cc_final: 0.8581 (m-10) REVERT: E 42 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8904 (mmmm) REVERT: E 90 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8256 (t) REVERT: E 94 TYR cc_start: 0.8430 (m-10) cc_final: 0.8174 (m-10) REVERT: E 165 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7680 (pp) REVERT: E 179 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 202 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6884 (mtm110) REVERT: E 223 ASP cc_start: 0.8968 (p0) cc_final: 0.8642 (p0) REVERT: G 12 ARG cc_start: 0.8889 (ptp-170) cc_final: 0.8446 (ptp90) REVERT: G 31 LYS cc_start: 0.9219 (tttp) cc_final: 0.8858 (tptm) REVERT: G 35 ASP cc_start: 0.8794 (m-30) cc_final: 0.8310 (m-30) outliers start: 48 outliers final: 28 residues processed: 252 average time/residue: 0.0840 time to fit residues: 29.7390 Evaluate side-chains 222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN G 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085067 restraints weight = 17546.880| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.02 r_work: 0.3122 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9147 Z= 0.206 Angle : 0.612 8.608 12415 Z= 0.314 Chirality : 0.044 0.245 1420 Planarity : 0.004 0.046 1551 Dihedral : 4.582 37.108 1256 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.61 % Allowed : 17.15 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1110 helix: 1.77 (0.27), residues: 384 sheet: -1.40 (0.29), residues: 255 loop : -1.26 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 134 TYR 0.015 0.001 TYR A 235 PHE 0.016 0.002 PHE E 212 TRP 0.016 0.001 TRP L 21 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 9145) covalent geometry : angle 0.61075 / 0.31 (12411) SS BOND : bond 0.00329 / 0.17 ( 2) SS BOND : angle 1.95806 / 1.11 ( 4) hydrogen bonds : bond 0.03573 / 2.50 ( 416) hydrogen bonds : angle 4.09659 / 2.98 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8201 (tt) REVERT: R 205 LEU cc_start: 0.9293 (tp) cc_final: 0.9025 (tt) REVERT: R 239 GLN cc_start: 0.8410 (tp40) cc_final: 0.8083 (tm-30) REVERT: A 26 GLU cc_start: 0.8472 (tp30) cc_final: 0.7986 (tp30) REVERT: A 28 GLN cc_start: 0.8632 (tp40) cc_final: 0.8355 (tp40) REVERT: A 198 LYS cc_start: 0.9320 (mmtt) cc_final: 0.9061 (mtmm) REVERT: B 135 GLU cc_start: 0.8818 (mp0) cc_final: 0.8581 (mp0) REVERT: B 203 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8828 (pp) REVERT: B 220 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: B 302 TRP cc_start: 0.9222 (m100) cc_final: 0.8596 (m-10) REVERT: B 334 THR cc_start: 0.9524 (m) cc_final: 0.9098 (p) REVERT: B 344 TRP cc_start: 0.8915 (m100) cc_final: 0.8557 (m-10) REVERT: E 42 LYS cc_start: 0.9236 (mmmm) cc_final: 0.9036 (mmmm) REVERT: E 90 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (t) REVERT: E 165 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7895 (pp) REVERT: E 179 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 192 MET cc_start: 0.7614 (ptm) cc_final: 0.6782 (ppp) REVERT: E 218 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7469 (tpp-160) REVERT: E 220 GLU cc_start: 0.7978 (mp0) cc_final: 0.7294 (mp0) REVERT: E 223 ASP cc_start: 0.8916 (p0) cc_final: 0.8511 (p0) REVERT: G 31 LYS cc_start: 0.9267 (tttp) cc_final: 0.8940 (tptm) REVERT: G 35 ASP cc_start: 0.8894 (m-30) cc_final: 0.8371 (m-30) outliers start: 54 outliers final: 38 residues processed: 240 average time/residue: 0.0800 time to fit residues: 27.1014 Evaluate side-chains 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.116464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088854 restraints weight = 17274.999| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.08 r_work: 0.3104 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9147 Z= 0.217 Angle : 0.610 7.863 12415 Z= 0.315 Chirality : 0.044 0.156 1420 Planarity : 0.004 0.058 1551 Dihedral : 4.616 42.507 1256 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.61 % Allowed : 19.33 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1110 helix: 1.68 (0.27), residues: 390 sheet: -1.33 (0.29), residues: 261 loop : -1.21 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 12 TYR 0.016 0.001 TYR R 199 PHE 0.017 0.002 PHE E 212 TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 9145) covalent geometry : angle 0.60897 / 0.31 (12411) SS BOND : bond 0.00235 / 0.12 ( 2) SS BOND : angle 1.88646 / 1.08 ( 4) hydrogen bonds : bond 0.03623 / 2.52 ( 416) hydrogen bonds : angle 4.14992 / 3.03 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8232 (tt) REVERT: R 93 CYS cc_start: 0.8392 (t) cc_final: 0.8159 (t) REVERT: R 97 ASP cc_start: 0.8360 (t70) cc_final: 0.8042 (t0) REVERT: R 205 LEU cc_start: 0.9295 (tp) cc_final: 0.9036 (tt) REVERT: R 239 GLN cc_start: 0.8444 (tp40) cc_final: 0.8195 (tm-30) REVERT: L 27 MET cc_start: 0.8254 (mmm) cc_final: 0.7966 (mmm) REVERT: A 26 GLU cc_start: 0.8426 (tp30) cc_final: 0.7987 (mm-30) REVERT: A 28 GLN cc_start: 0.8674 (tp40) cc_final: 0.8419 (tp40) REVERT: A 198 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9095 (mtmm) REVERT: B 135 GLU cc_start: 0.8815 (mp0) cc_final: 0.8606 (mp0) REVERT: B 203 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 220 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: B 302 TRP cc_start: 0.9264 (m100) cc_final: 0.8585 (m-10) REVERT: B 334 THR cc_start: 0.9551 (m) cc_final: 0.9064 (p) REVERT: B 344 TRP cc_start: 0.8944 (m100) cc_final: 0.8632 (m-10) REVERT: E 42 LYS cc_start: 0.9239 (mmmm) cc_final: 0.9030 (mmmm) REVERT: E 90 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8274 (t) REVERT: E 160 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8432 (mtm-85) REVERT: E 165 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7955 (pp) REVERT: E 179 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 192 MET cc_start: 0.7504 (ptm) cc_final: 0.6770 (ppp) REVERT: E 223 ASP cc_start: 0.8925 (p0) cc_final: 0.8665 (p0) REVERT: E 239 PHE cc_start: 0.8875 (m-80) cc_final: 0.8628 (m-10) REVERT: G 12 ARG cc_start: 0.8687 (ptp90) cc_final: 0.8123 (ptp90) REVERT: G 13 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8697 (mmtm) REVERT: G 31 LYS cc_start: 0.9293 (tttp) cc_final: 0.8935 (tptm) REVERT: G 35 ASP cc_start: 0.8954 (m-30) cc_final: 0.8382 (m-30) REVERT: G 47 ASP cc_start: 0.8765 (t0) cc_final: 0.8453 (t0) outliers start: 54 outliers final: 41 residues processed: 230 average time/residue: 0.0836 time to fit residues: 26.9352 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.0470 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 261 ASN A 336 ASN B 147 HIS B 273 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089775 restraints weight = 16873.842| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.95 r_work: 0.3199 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9147 Z= 0.113 Angle : 0.559 7.381 12415 Z= 0.286 Chirality : 0.042 0.168 1420 Planarity : 0.004 0.054 1551 Dihedral : 4.287 39.425 1256 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.78 % Allowed : 19.96 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1110 helix: 1.94 (0.27), residues: 385 sheet: -1.31 (0.29), residues: 264 loop : -1.01 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 12 TYR 0.017 0.001 TYR R 199 PHE 0.016 0.001 PHE E 28 TRP 0.011 0.001 TRP B 174 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9145) covalent geometry : angle 0.55841 / 0.29 (12411) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 1.40734 / 0.81 ( 4) hydrogen bonds : bond 0.03254 / 2.28 ( 416) hydrogen bonds : angle 3.94429 / 2.86 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8254 (tt) REVERT: R 97 ASP cc_start: 0.8412 (t70) cc_final: 0.8072 (t0) REVERT: R 205 LEU cc_start: 0.9251 (tp) cc_final: 0.8952 (tt) REVERT: R 212 MET cc_start: 0.8242 (tpp) cc_final: 0.6958 (ttt) REVERT: R 239 GLN cc_start: 0.8367 (tp40) cc_final: 0.8091 (tm-30) REVERT: R 286 TYR cc_start: 0.8319 (t80) cc_final: 0.7855 (t80) REVERT: R 295 ASP cc_start: 0.7948 (p0) cc_final: 0.6928 (p0) REVERT: L 27 MET cc_start: 0.8183 (mmm) cc_final: 0.7794 (mmm) REVERT: A 26 GLU cc_start: 0.8309 (tp30) cc_final: 0.7862 (tp30) REVERT: A 28 GLN cc_start: 0.8605 (tp40) cc_final: 0.8350 (tp40) REVERT: A 59 MET cc_start: 0.9034 (ppp) cc_final: 0.8360 (ppp) REVERT: B 74 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8800 (mt) REVERT: B 135 GLU cc_start: 0.8807 (mp0) cc_final: 0.8575 (mp0) REVERT: B 193 MET cc_start: 0.8323 (mmt) cc_final: 0.7932 (mmm) REVERT: B 203 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 216 TRP cc_start: 0.8731 (m100) cc_final: 0.8385 (m100) REVERT: B 302 TRP cc_start: 0.9139 (m100) cc_final: 0.8508 (m-10) REVERT: B 334 THR cc_start: 0.9437 (m) cc_final: 0.9069 (p) REVERT: B 344 TRP cc_start: 0.8922 (m100) cc_final: 0.8590 (m-10) REVERT: E 28 PHE cc_start: 0.8832 (t80) cc_final: 0.8620 (t80) REVERT: E 42 LYS cc_start: 0.9269 (mmmm) cc_final: 0.9041 (mmmm) REVERT: E 66 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7278 (ptm160) REVERT: E 90 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8238 (t) REVERT: E 165 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7959 (pp) REVERT: E 192 MET cc_start: 0.7211 (ptm) cc_final: 0.6476 (ppp) REVERT: E 218 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7960 (tpp-160) REVERT: E 239 PHE cc_start: 0.8824 (m-80) cc_final: 0.8521 (m-10) REVERT: G 12 ARG cc_start: 0.8755 (ptp90) cc_final: 0.8363 (ptp90) REVERT: G 19 LYS cc_start: 0.9166 (mttp) cc_final: 0.8958 (mtmm) REVERT: G 31 LYS cc_start: 0.9301 (tttp) cc_final: 0.8933 (tptm) REVERT: G 35 ASP cc_start: 0.8938 (m-30) cc_final: 0.8352 (m-30) REVERT: G 45 LYS cc_start: 0.9088 (mppt) cc_final: 0.8848 (tppt) REVERT: G 47 ASP cc_start: 0.8735 (t0) cc_final: 0.8344 (t0) outliers start: 46 outliers final: 25 residues processed: 240 average time/residue: 0.0873 time to fit residues: 29.1372 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 0.0050 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089054 restraints weight = 17044.479| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.96 r_work: 0.3183 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9147 Z= 0.137 Angle : 0.587 9.761 12415 Z= 0.298 Chirality : 0.043 0.269 1420 Planarity : 0.004 0.056 1551 Dihedral : 4.277 40.208 1256 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.99 % Allowed : 20.06 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1110 helix: 2.06 (0.27), residues: 385 sheet: -1.18 (0.30), residues: 264 loop : -0.95 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 12 TYR 0.016 0.001 TYR R 199 PHE 0.014 0.001 PHE E 212 TRP 0.015 0.001 TRP R 106 HIS 0.006 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9145) covalent geometry : angle 0.58644 / 0.30 (12411) SS BOND : bond 0.00144 / 0.08 ( 2) SS BOND : angle 1.47997 / 0.85 ( 4) hydrogen bonds : bond 0.03275 / 2.28 ( 416) hydrogen bonds : angle 3.90165 / 2.84 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8247 (tt) REVERT: R 205 LEU cc_start: 0.9269 (tp) cc_final: 0.9021 (tt) REVERT: R 239 GLN cc_start: 0.8374 (tp40) cc_final: 0.8101 (tm-30) REVERT: R 286 TYR cc_start: 0.8339 (t80) cc_final: 0.7868 (t80) REVERT: R 295 ASP cc_start: 0.8053 (p0) cc_final: 0.7040 (p0) REVERT: A 26 GLU cc_start: 0.8300 (tp30) cc_final: 0.7860 (tp30) REVERT: A 28 GLN cc_start: 0.8610 (tp40) cc_final: 0.8330 (tp40) REVERT: B 106 MET cc_start: 0.9363 (mtp) cc_final: 0.9032 (mtp) REVERT: B 193 MET cc_start: 0.8359 (mmt) cc_final: 0.7972 (mmm) REVERT: B 203 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 216 TRP cc_start: 0.8760 (m100) cc_final: 0.8364 (m100) REVERT: B 220 GLU cc_start: 0.8530 (pm20) cc_final: 0.8112 (pm20) REVERT: B 302 TRP cc_start: 0.9146 (m100) cc_final: 0.8488 (m-10) REVERT: B 334 THR cc_start: 0.9465 (m) cc_final: 0.9070 (p) REVERT: B 344 TRP cc_start: 0.8933 (m100) cc_final: 0.8574 (m-10) REVERT: E 28 PHE cc_start: 0.8882 (t80) cc_final: 0.8655 (t80) REVERT: E 42 LYS cc_start: 0.9256 (mmmm) cc_final: 0.9017 (mmmm) REVERT: E 66 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: E 90 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8265 (t) REVERT: E 140 MET cc_start: 0.8134 (pmm) cc_final: 0.7749 (pmm) REVERT: E 165 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7950 (pp) REVERT: E 192 MET cc_start: 0.7337 (ptm) cc_final: 0.6658 (ppp) REVERT: E 218 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7666 (tpp-160) REVERT: E 220 GLU cc_start: 0.8264 (mp0) cc_final: 0.7831 (pm20) REVERT: E 229 CYS cc_start: 0.8800 (p) cc_final: 0.8492 (p) REVERT: E 239 PHE cc_start: 0.8847 (m-80) cc_final: 0.8635 (m-10) REVERT: G 12 ARG cc_start: 0.8669 (ptp90) cc_final: 0.8336 (ptp90) REVERT: G 31 LYS cc_start: 0.9299 (tttp) cc_final: 0.8922 (tptm) REVERT: G 35 ASP cc_start: 0.8953 (m-30) cc_final: 0.8360 (m-30) REVERT: G 45 LYS cc_start: 0.9084 (mppt) cc_final: 0.8831 (tppt) REVERT: G 47 ASP cc_start: 0.8729 (t0) cc_final: 0.8337 (t0) outliers start: 48 outliers final: 31 residues processed: 227 average time/residue: 0.0782 time to fit residues: 25.1354 Evaluate side-chains 222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN B 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.118441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088101 restraints weight = 16950.401| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.94 r_work: 0.3167 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9147 Z= 0.148 Angle : 0.605 8.883 12415 Z= 0.307 Chirality : 0.044 0.268 1420 Planarity : 0.004 0.058 1551 Dihedral : 4.288 40.802 1256 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.57 % Allowed : 20.48 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1110 helix: 2.05 (0.27), residues: 385 sheet: -1.08 (0.30), residues: 263 loop : -0.96 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 12 TYR 0.015 0.001 TYR R 199 PHE 0.015 0.001 PHE E 203 TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9145) covalent geometry : angle 0.60469 / 0.31 (12411) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 1.54753 / 0.89 ( 4) hydrogen bonds : bond 0.03356 / 2.35 ( 416) hydrogen bonds : angle 3.93995 / 2.87 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (tt) REVERT: R 205 LEU cc_start: 0.9292 (tp) cc_final: 0.9042 (tt) REVERT: R 212 MET cc_start: 0.8256 (tpp) cc_final: 0.6941 (ttp) REVERT: R 239 GLN cc_start: 0.8354 (tp40) cc_final: 0.8144 (tm-30) REVERT: R 286 TYR cc_start: 0.8365 (t80) cc_final: 0.7886 (t80) REVERT: L 27 MET cc_start: 0.8168 (mmm) cc_final: 0.7879 (mmm) REVERT: A 14 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: A 28 GLN cc_start: 0.8553 (tp40) cc_final: 0.8263 (tp40) REVERT: A 59 MET cc_start: 0.9057 (ppp) cc_final: 0.8462 (ppp) REVERT: B 134 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8467 (ttp80) REVERT: B 193 MET cc_start: 0.8386 (mmt) cc_final: 0.7989 (mmm) REVERT: B 203 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8804 (pp) REVERT: B 220 GLU cc_start: 0.8558 (pm20) cc_final: 0.8109 (pm20) REVERT: B 302 TRP cc_start: 0.9169 (m100) cc_final: 0.8498 (m-10) REVERT: B 334 THR cc_start: 0.9478 (m) cc_final: 0.9028 (p) REVERT: B 344 TRP cc_start: 0.8935 (m100) cc_final: 0.8564 (m-10) REVERT: E 42 LYS cc_start: 0.9260 (mmmm) cc_final: 0.9015 (mmmm) REVERT: E 66 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: E 90 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8272 (t) REVERT: E 140 MET cc_start: 0.7984 (pmm) cc_final: 0.7770 (pmm) REVERT: E 192 MET cc_start: 0.7306 (ptm) cc_final: 0.6710 (ppp) REVERT: E 202 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7350 (mtp-110) REVERT: E 218 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7456 (tpp-160) REVERT: E 223 ASP cc_start: 0.8801 (p0) cc_final: 0.8536 (p0) REVERT: E 229 CYS cc_start: 0.8775 (p) cc_final: 0.8501 (p) REVERT: G 12 ARG cc_start: 0.8746 (ptp90) cc_final: 0.8527 (ptp90) REVERT: G 13 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8561 (mmtm) REVERT: G 35 ASP cc_start: 0.8965 (m-30) cc_final: 0.8639 (m-30) REVERT: G 45 LYS cc_start: 0.9111 (mppt) cc_final: 0.8844 (tppt) REVERT: G 47 ASP cc_start: 0.8750 (t0) cc_final: 0.8321 (t0) outliers start: 44 outliers final: 31 residues processed: 222 average time/residue: 0.0810 time to fit residues: 25.2593 Evaluate side-chains 218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088815 restraints weight = 16757.976| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.93 r_work: 0.3181 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9147 Z= 0.136 Angle : 0.615 9.180 12415 Z= 0.309 Chirality : 0.044 0.263 1420 Planarity : 0.004 0.059 1551 Dihedral : 4.254 39.920 1256 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.74 % Allowed : 21.62 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1110 helix: 2.06 (0.27), residues: 385 sheet: -0.96 (0.31), residues: 257 loop : -0.96 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 17 TYR 0.015 0.001 TYR R 199 PHE 0.040 0.001 PHE E 239 TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9145) covalent geometry : angle 0.61415 / 0.31 (12411) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 1.49496 / 0.86 ( 4) hydrogen bonds : bond 0.03352 / 2.34 ( 416) hydrogen bonds : angle 3.94541 / 2.86 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8229 (tt) REVERT: R 155 MET cc_start: 0.6060 (tpt) cc_final: 0.5650 (tpp) REVERT: R 205 LEU cc_start: 0.9242 (tp) cc_final: 0.8997 (tt) REVERT: R 212 MET cc_start: 0.8245 (tpp) cc_final: 0.6949 (ttp) REVERT: R 239 GLN cc_start: 0.8354 (tp40) cc_final: 0.8150 (tm-30) REVERT: R 286 TYR cc_start: 0.8353 (t80) cc_final: 0.7899 (t80) REVERT: L 27 MET cc_start: 0.8149 (mmm) cc_final: 0.7841 (mmm) REVERT: A 14 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: A 26 GLU cc_start: 0.8272 (tp30) cc_final: 0.7942 (mm-30) REVERT: A 28 GLN cc_start: 0.8545 (tp40) cc_final: 0.8252 (tp40) REVERT: A 59 MET cc_start: 0.9001 (ppp) cc_final: 0.8509 (ppp) REVERT: B 106 MET cc_start: 0.9348 (mtp) cc_final: 0.9133 (mtp) REVERT: B 134 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8514 (ptm-80) REVERT: B 193 MET cc_start: 0.8362 (mmt) cc_final: 0.7983 (mmm) REVERT: B 203 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 220 GLU cc_start: 0.8576 (pm20) cc_final: 0.8146 (pm20) REVERT: B 302 TRP cc_start: 0.9153 (m100) cc_final: 0.8514 (m-10) REVERT: B 334 THR cc_start: 0.9454 (m) cc_final: 0.9074 (p) REVERT: B 344 TRP cc_start: 0.8925 (m100) cc_final: 0.8564 (m-10) REVERT: E 42 LYS cc_start: 0.9292 (mmmm) cc_final: 0.9033 (mmmm) REVERT: E 66 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.5648 (ptm160) REVERT: E 90 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8239 (t) REVERT: E 192 MET cc_start: 0.7332 (ptm) cc_final: 0.6958 (ppp) REVERT: E 202 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7340 (mtp-110) REVERT: E 218 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7512 (tpp-160) REVERT: E 223 ASP cc_start: 0.8812 (p0) cc_final: 0.8298 (p0) REVERT: E 229 CYS cc_start: 0.8767 (p) cc_final: 0.8498 (p) REVERT: G 13 LYS cc_start: 0.8840 (mmtm) cc_final: 0.8566 (mmtm) REVERT: G 28 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8165 (mmmt) REVERT: G 45 LYS cc_start: 0.9111 (mppt) cc_final: 0.8843 (tppt) REVERT: G 47 ASP cc_start: 0.8749 (t0) cc_final: 0.8305 (t0) outliers start: 36 outliers final: 29 residues processed: 215 average time/residue: 0.0862 time to fit residues: 25.8932 Evaluate side-chains 209 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.119711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089189 restraints weight = 16968.700| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.97 r_work: 0.3195 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9147 Z= 0.126 Angle : 0.628 10.516 12415 Z= 0.313 Chirality : 0.044 0.259 1420 Planarity : 0.004 0.080 1551 Dihedral : 4.187 38.089 1256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.33 % Allowed : 22.77 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1110 helix: 2.07 (0.27), residues: 385 sheet: -0.89 (0.31), residues: 257 loop : -0.92 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 66 TYR 0.013 0.001 TYR R 199 PHE 0.026 0.001 PHE E 239 TRP 0.011 0.001 TRP B 174 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9145) covalent geometry : angle 0.62733 / 0.31 (12411) SS BOND : bond 0.00088 / 0.05 ( 2) SS BOND : angle 1.41771 / 0.81 ( 4) hydrogen bonds : bond 0.03265 / 2.28 ( 416) hydrogen bonds : angle 3.93190 / 2.84 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8238 (tt) REVERT: R 155 MET cc_start: 0.6025 (tpt) cc_final: 0.5621 (tpp) REVERT: R 205 LEU cc_start: 0.9243 (tp) cc_final: 0.8988 (tt) REVERT: R 212 MET cc_start: 0.8184 (tpp) cc_final: 0.6924 (ttp) REVERT: R 239 GLN cc_start: 0.8354 (tp40) cc_final: 0.8114 (tm-30) REVERT: R 286 TYR cc_start: 0.8342 (t80) cc_final: 0.7908 (t80) REVERT: L 27 MET cc_start: 0.8110 (mmm) cc_final: 0.7712 (mmm) REVERT: A 14 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: A 26 GLU cc_start: 0.8318 (tp30) cc_final: 0.8020 (mm-30) REVERT: A 28 GLN cc_start: 0.8531 (tp40) cc_final: 0.8236 (tp40) REVERT: A 57 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8592 (mmmt) REVERT: A 59 MET cc_start: 0.8917 (ppp) cc_final: 0.8534 (ppp) REVERT: B 134 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8435 (ttp80) REVERT: B 193 MET cc_start: 0.8293 (mmt) cc_final: 0.7804 (mmm) REVERT: B 203 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 220 GLU cc_start: 0.8605 (pm20) cc_final: 0.8274 (pm20) REVERT: B 222 MET cc_start: 0.8374 (ppp) cc_final: 0.7862 (ppp) REVERT: B 302 TRP cc_start: 0.9106 (m100) cc_final: 0.8503 (m-10) REVERT: B 334 THR cc_start: 0.9426 (m) cc_final: 0.9080 (p) REVERT: B 344 TRP cc_start: 0.8901 (m100) cc_final: 0.8564 (m-10) REVERT: E 42 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9062 (mmmm) REVERT: E 45 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: E 51 SER cc_start: 0.7975 (m) cc_final: 0.7714 (p) REVERT: E 90 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8205 (t) REVERT: E 192 MET cc_start: 0.7093 (ptm) cc_final: 0.6776 (ppp) REVERT: E 223 ASP cc_start: 0.8778 (p0) cc_final: 0.8495 (p0) REVERT: E 229 CYS cc_start: 0.8758 (p) cc_final: 0.8486 (p) REVERT: G 35 ASP cc_start: 0.8792 (m-30) cc_final: 0.8368 (m-30) REVERT: G 45 LYS cc_start: 0.9114 (mppt) cc_final: 0.8868 (tppt) REVERT: G 47 ASP cc_start: 0.8742 (t0) cc_final: 0.8318 (t0) outliers start: 32 outliers final: 24 residues processed: 212 average time/residue: 0.0734 time to fit residues: 22.4162 Evaluate side-chains 208 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090601 restraints weight = 16794.183| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.95 r_work: 0.3220 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9147 Z= 0.121 Angle : 0.639 14.443 12415 Z= 0.315 Chirality : 0.044 0.258 1420 Planarity : 0.004 0.060 1551 Dihedral : 4.091 36.065 1256 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.53 % Allowed : 22.66 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1110 helix: 2.13 (0.27), residues: 380 sheet: -0.76 (0.31), residues: 256 loop : -0.92 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.012 0.001 TYR R 199 PHE 0.015 0.001 PHE E 239 TRP 0.011 0.001 TRP B 174 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9145) covalent geometry : angle 0.63863 / 0.32 (12411) SS BOND : bond 0.00076 / 0.04 ( 2) SS BOND : angle 1.42724 / 0.82 ( 4) hydrogen bonds : bond 0.03230 / 2.26 ( 416) hydrogen bonds : angle 3.90206 / 2.81 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.39 seconds wall clock time: 37 minutes 1.65 seconds (2221.65 seconds total)