Starting phenix.real_space_refine on Tue Mar 3 22:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0q_34414/03_2026/8h0q_34414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0q_34414/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2026/8h0q_34414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2026/8h0q_34414.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2026/8h0q_34414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2026/8h0q_34414.cif" } 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-5986/lib/python3.9/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: 1.94, per 1000 atoms: 0.22 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: 0.61 Conformation dependent library (CDL) restraints added in 344.1 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: 0.20 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: 1.50 Time building geometry restraints manager: 0.87 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 - 12.99: 5260 12.99 - 25.98: 191 25.98 - 38.97: 84 38.97 - 51.97: 20 51.97 - 64.96: 15 Dihedral angle restraints: 5570 sinusoidal: 2267 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 5567 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: 1.500 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 9.284 64.956 3426 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 covalent geometry : bond 0.01862 ( 9145) covalent geometry : angle 0.58930 (12411) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.45896 ( 4) hydrogen bonds : bond 0.13930 ( 416) hydrogen bonds : angle 5.09501 ( 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 : 0.337 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: 0.1167 time to fit residues: 62.7212 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090397 restraints weight = 17121.106| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.00 r_work: 0.3221 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9147 Z= 0.308 Angle : 0.737 7.648 12415 Z= 0.381 Chirality : 0.047 0.207 1420 Planarity : 0.005 0.044 1551 Dihedral : 6.799 54.521 1425 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.09 % Allowed : 15.07 % Favored : 79.83 % 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: -0.96 (0.25), residues: 1110 helix: 1.21 (0.26), residues: 387 sheet: -1.58 (0.28), residues: 271 loop : -1.62 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 191 TYR 0.017 0.002 TYR R 199 PHE 0.020 0.002 PHE R 275 TRP 0.019 0.002 TRP L 21 HIS 0.009 0.002 HIS R 281 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 9145) covalent geometry : angle 0.73655 (12411) SS BOND : bond 0.00464 ( 2) SS BOND : angle 2.04171 ( 4) hydrogen bonds : bond 0.04014 ( 416) hydrogen bonds : angle 4.35144 ( 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 289 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8134 (tt) REVERT: R 163 PHE cc_start: 0.7546 (t80) cc_final: 0.7302 (t80) REVERT: R 205 LEU cc_start: 0.9292 (tp) cc_final: 0.9025 (tt) REVERT: R 242 TYR cc_start: 0.8064 (m-10) cc_final: 0.7863 (m-10) REVERT: R 286 TYR cc_start: 0.8349 (t80) cc_final: 0.7903 (t80) REVERT: L 23 VAL cc_start: 0.9266 (t) cc_final: 0.9053 (m) REVERT: L 26 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6765 (pp) REVERT: A 26 GLU cc_start: 0.8391 (tp30) cc_final: 0.8187 (mm-30) REVERT: A 28 GLN cc_start: 0.8580 (tp40) cc_final: 0.8320 (tp40) REVERT: A 34 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 198 LYS cc_start: 0.9332 (mmtt) cc_final: 0.9072 (mtmm) REVERT: A 253 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.8570 (m110) REVERT: B 135 GLU cc_start: 0.8771 (mp0) cc_final: 0.8558 (mp0) REVERT: B 203 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8798 (pp) REVERT: B 220 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: B 285 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8491 (ttmm) REVERT: B 302 TRP cc_start: 0.9160 (m100) cc_final: 0.8614 (m-10) REVERT: B 344 TRP cc_start: 0.8931 (m100) cc_final: 0.8583 (m-10) REVERT: E 2 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7732 (mm-40) REVERT: E 42 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8945 (mmmm) REVERT: E 45 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8311 (mt-10) REVERT: E 72 ASP cc_start: 0.7407 (t70) cc_final: 0.6710 (p0) REVERT: E 90 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8448 (t) REVERT: E 138 ILE cc_start: 0.8410 (mm) cc_final: 0.8087 (mm) REVERT: E 165 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7549 (pp) REVERT: E 192 MET cc_start: 0.7307 (ptm) cc_final: 0.6861 (ptm) REVERT: E 202 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6702 (mtm110) REVERT: E 220 GLU cc_start: 0.8245 (mp0) cc_final: 0.7936 (mp0) REVERT: E 223 ASP cc_start: 0.9023 (p0) cc_final: 0.8527 (p0) REVERT: G 12 ARG cc_start: 0.8914 (ptp-170) cc_final: 0.8470 (ptp90) REVERT: G 31 LYS cc_start: 0.9183 (tttp) cc_final: 0.8929 (tptm) REVERT: G 35 ASP cc_start: 0.8754 (m-30) cc_final: 0.8391 (m-30) outliers start: 49 outliers final: 26 residues processed: 274 average time/residue: 0.0877 time to fit residues: 33.2364 Evaluate side-chains 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 285 LEU 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 93 ASN 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 157 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 194 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN B 59 HIS B 93 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN G 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091125 restraints weight = 17243.799| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.07 r_work: 0.3189 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9147 Z= 0.159 Angle : 0.581 8.432 12415 Z= 0.298 Chirality : 0.044 0.225 1420 Planarity : 0.004 0.043 1551 Dihedral : 5.848 47.239 1424 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.51 % Allowed : 16.01 % Favored : 78.48 % 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: -0.53 (0.26), residues: 1110 helix: 1.70 (0.27), residues: 390 sheet: -1.63 (0.28), residues: 269 loop : -1.31 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 297 TYR 0.012 0.001 TYR A 235 PHE 0.015 0.001 PHE A 228 TRP 0.031 0.001 TRP L 21 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9145) covalent geometry : angle 0.57915 (12411) SS BOND : bond 0.00487 ( 2) SS BOND : angle 2.78247 ( 4) hydrogen bonds : bond 0.03331 ( 416) hydrogen bonds : angle 3.96490 ( 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: 53 poor density : 214 time to evaluate : 0.299 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: 0.8551 (OUTLIER) cc_final: 0.8253 (tt) REVERT: R 90 LEU cc_start: 0.8662 (mt) cc_final: 0.8454 (mt) REVERT: R 205 LEU cc_start: 0.9268 (tp) cc_final: 0.9012 (tt) REVERT: R 286 TYR cc_start: 0.8309 (t80) cc_final: 0.7850 (t80) REVERT: L 26 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7164 (pp) REVERT: A 26 GLU cc_start: 0.8414 (tp30) cc_final: 0.8202 (mm-30) REVERT: A 28 GLN cc_start: 0.8576 (tp40) cc_final: 0.8332 (tp40) REVERT: A 193 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8075 (mtmt) REVERT: A 198 LYS cc_start: 0.9324 (mmtt) cc_final: 0.9052 (mtmm) REVERT: B 135 GLU cc_start: 0.8761 (mp0) cc_final: 0.8533 (mp0) REVERT: B 203 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8816 (pp) REVERT: B 220 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: B 285 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8055 (ttmm) REVERT: B 294 TYR cc_start: 0.8837 (m-80) cc_final: 0.8571 (m-80) REVERT: B 302 TRP cc_start: 0.9137 (m100) cc_final: 0.8543 (m-10) REVERT: B 344 TRP cc_start: 0.8912 (m100) cc_final: 0.8600 (m-10) REVERT: E 42 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8928 (mmmm) REVERT: E 82 MET cc_start: 0.7673 (pmm) cc_final: 0.7453 (ptp) REVERT: E 90 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8267 (t) REVERT: E 165 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7771 (pp) REVERT: E 179 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 202 ARG cc_start: 0.7080 (mtm110) cc_final: 0.6765 (mtm110) REVERT: E 218 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7942 (mmp80) REVERT: E 220 GLU cc_start: 0.8284 (mp0) cc_final: 0.7971 (mp0) REVERT: E 223 ASP cc_start: 0.9031 (p0) cc_final: 0.8525 (p0) REVERT: G 31 LYS cc_start: 0.9218 (tttp) cc_final: 0.8898 (tptm) REVERT: G 35 ASP cc_start: 0.8807 (m-30) cc_final: 0.8365 (m-30) outliers start: 53 outliers final: 31 residues processed: 249 average time/residue: 0.0845 time to fit residues: 29.3289 Evaluate side-chains 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 240 SER Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain L residue 26 LEU 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 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 91 THR 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 16 GLU 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: 3.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 GLN A 202 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 336 ASN B 93 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.118895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090551 restraints weight = 17446.046| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.10 r_work: 0.3172 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9147 Z= 0.146 Angle : 0.562 7.552 12415 Z= 0.287 Chirality : 0.042 0.165 1420 Planarity : 0.004 0.048 1551 Dihedral : 5.620 44.748 1424 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.30 % Allowed : 18.50 % Favored : 76.20 % 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: -0.37 (0.26), residues: 1110 helix: 1.73 (0.27), residues: 397 sheet: -1.50 (0.28), residues: 269 loop : -1.20 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 12 TYR 0.013 0.001 TYR R 199 PHE 0.015 0.001 PHE E 203 TRP 0.014 0.001 TRP L 21 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9145) covalent geometry : angle 0.56092 (12411) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.76178 ( 4) hydrogen bonds : bond 0.03240 ( 416) hydrogen bonds : angle 3.93031 ( 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 260 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8239 (tt) REVERT: R 90 LEU cc_start: 0.8662 (mt) cc_final: 0.8459 (mt) REVERT: R 205 LEU cc_start: 0.9272 (tp) cc_final: 0.9004 (tt) REVERT: R 286 TYR cc_start: 0.8317 (t80) cc_final: 0.7871 (t80) REVERT: R 295 ASP cc_start: 0.7766 (p0) cc_final: 0.7189 (p0) REVERT: A 26 GLU cc_start: 0.8406 (tp30) cc_final: 0.7970 (tp30) REVERT: A 28 GLN cc_start: 0.8616 (tp40) cc_final: 0.8328 (tp40) REVERT: A 198 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9055 (mtmm) REVERT: A 315 ASP cc_start: 0.8706 (t0) cc_final: 0.8444 (t0) REVERT: B 203 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 220 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: B 302 TRP cc_start: 0.9147 (m100) cc_final: 0.8537 (m-10) REVERT: B 306 LYS cc_start: 0.9140 (mmtp) cc_final: 0.8909 (mmtt) REVERT: B 334 THR cc_start: 0.9396 (m) cc_final: 0.9083 (p) REVERT: B 344 TRP cc_start: 0.8896 (m100) cc_final: 0.8595 (m-10) REVERT: E 42 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8935 (mmmm) REVERT: E 90 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8334 (t) REVERT: E 165 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7904 (pp) REVERT: E 179 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 192 MET cc_start: 0.7361 (ptm) cc_final: 0.6529 (ppp) REVERT: E 202 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6962 (mtm110) REVERT: E 218 ARG cc_start: 0.8310 (mmp80) cc_final: 0.8052 (mmp80) REVERT: E 220 GLU cc_start: 0.8308 (mp0) cc_final: 0.8073 (mp0) REVERT: E 223 ASP cc_start: 0.9019 (p0) cc_final: 0.8542 (p0) REVERT: G 12 ARG cc_start: 0.8730 (ptp90) cc_final: 0.8405 (ptp90) REVERT: G 31 LYS cc_start: 0.9232 (tttp) cc_final: 0.8895 (tptm) REVERT: G 35 ASP cc_start: 0.8847 (m-30) cc_final: 0.8329 (m-30) outliers start: 51 outliers final: 34 residues processed: 242 average time/residue: 0.0873 time to fit residues: 29.5201 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 76 ASN 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 282 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 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 321 SER 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 14 LEU Chi-restraints excluded: chain G residue 16 GLU 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: 0.7980 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 11 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN E 194 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088793 restraints weight = 17205.759| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.09 r_work: 0.3118 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9147 Z= 0.215 Angle : 0.612 8.383 12415 Z= 0.316 Chirality : 0.045 0.260 1420 Planarity : 0.004 0.063 1551 Dihedral : 5.611 55.371 1424 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.55 % Allowed : 17.46 % Favored : 75.99 % 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: -0.22 (0.26), residues: 1110 helix: 1.91 (0.27), residues: 384 sheet: -1.30 (0.30), residues: 259 loop : -1.17 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 12 TYR 0.016 0.001 TYR R 199 PHE 0.016 0.002 PHE E 212 TRP 0.013 0.001 TRP B 174 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9145) covalent geometry : angle 0.61108 (12411) SS BOND : bond 0.00226 ( 2) SS BOND : angle 1.83606 ( 4) hydrogen bonds : bond 0.03569 ( 416) hydrogen bonds : angle 4.16871 ( 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 256 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8207 (tt) REVERT: R 205 LEU cc_start: 0.9298 (tp) cc_final: 0.9044 (tt) REVERT: A 26 GLU cc_start: 0.8443 (tp30) cc_final: 0.7965 (tp30) REVERT: A 28 GLN cc_start: 0.8648 (tp40) cc_final: 0.8435 (tp40) REVERT: A 198 LYS cc_start: 0.9314 (mmtt) cc_final: 0.9105 (mtmm) REVERT: B 203 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8883 (pp) REVERT: B 220 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: B 302 TRP cc_start: 0.9264 (m100) cc_final: 0.8551 (m-10) REVERT: B 334 THR cc_start: 0.9470 (m) cc_final: 0.9059 (p) REVERT: B 344 TRP cc_start: 0.8925 (m100) cc_final: 0.8620 (m-10) REVERT: E 42 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8939 (mmmm) REVERT: E 79 PHE cc_start: 0.7858 (m-80) cc_final: 0.7642 (m-80) REVERT: E 90 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8330 (t) REVERT: E 165 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7998 (pp) REVERT: E 192 MET cc_start: 0.7423 (ptm) cc_final: 0.6642 (ppp) REVERT: E 223 ASP cc_start: 0.9004 (p0) cc_final: 0.8606 (p0) REVERT: G 12 ARG cc_start: 0.8648 (ptp90) cc_final: 0.8296 (ptp90) REVERT: G 13 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8533 (mmtm) REVERT: G 31 LYS cc_start: 0.9269 (tttp) cc_final: 0.8888 (tptm) REVERT: G 35 ASP cc_start: 0.8906 (m-30) cc_final: 0.8329 (m-30) REVERT: G 47 ASP cc_start: 0.8788 (t0) cc_final: 0.8464 (t0) outliers start: 63 outliers final: 43 residues processed: 234 average time/residue: 0.0742 time to fit residues: 24.9288 Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 268 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 282 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 A residue 344 CYS Chi-restraints excluded: chain B residue 11 GLN 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 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 278 ILE Chi-restraints excluded: chain B residue 321 SER 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 159 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 16 GLU 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: 5.9990 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 300 HIS ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 147 HIS E 76 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090080 restraints weight = 16915.047| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.94 r_work: 0.3202 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9147 Z= 0.118 Angle : 0.568 7.881 12415 Z= 0.289 Chirality : 0.042 0.180 1420 Planarity : 0.003 0.046 1551 Dihedral : 5.393 55.833 1424 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.89 % Allowed : 19.65 % Favored : 75.47 % 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: 2.01 (0.27), residues: 385 sheet: -1.32 (0.29), residues: 270 loop : -0.98 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 12 TYR 0.020 0.001 TYR R 199 PHE 0.023 0.001 PHE E 239 TRP 0.052 0.001 TRP L 21 HIS 0.005 0.001 HIS R 300 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9145) covalent geometry : angle 0.56707 (12411) SS BOND : bond 0.00173 ( 2) SS BOND : angle 1.43843 ( 4) hydrogen bonds : bond 0.03251 ( 416) hydrogen bonds : angle 3.96076 ( 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 246 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (tt) REVERT: R 97 ASP cc_start: 0.8387 (t70) cc_final: 0.7961 (t0) REVERT: R 205 LEU cc_start: 0.9242 (tp) cc_final: 0.8947 (tt) REVERT: R 212 MET cc_start: 0.8070 (tpp) cc_final: 0.6881 (ttm) REVERT: R 286 TYR cc_start: 0.8360 (t80) cc_final: 0.7882 (t80) REVERT: R 295 ASP cc_start: 0.8025 (p0) cc_final: 0.6942 (p0) REVERT: A 26 GLU cc_start: 0.8322 (tp30) cc_final: 0.7861 (tp30) REVERT: A 28 GLN cc_start: 0.8594 (tp40) cc_final: 0.8351 (tp40) REVERT: B 74 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 135 GLU cc_start: 0.8808 (mp0) cc_final: 0.8589 (mp0) REVERT: B 203 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8828 (pp) REVERT: B 216 TRP cc_start: 0.8759 (m100) cc_final: 0.8343 (m100) REVERT: B 220 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8453 (pm20) REVERT: B 302 TRP cc_start: 0.9153 (m100) cc_final: 0.8495 (m-10) REVERT: B 334 THR cc_start: 0.9353 (m) cc_final: 0.9096 (p) REVERT: B 344 TRP cc_start: 0.8904 (m100) cc_final: 0.8584 (m-10) REVERT: E 42 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8928 (mmmm) REVERT: E 79 PHE cc_start: 0.7864 (m-80) cc_final: 0.7646 (m-80) REVERT: E 90 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8290 (t) REVERT: E 165 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7916 (pp) REVERT: E 192 MET cc_start: 0.6995 (ptm) cc_final: 0.6305 (ppp) REVERT: G 12 ARG cc_start: 0.8730 (ptp90) cc_final: 0.8417 (ptp90) REVERT: G 13 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8479 (mmtm) REVERT: G 31 LYS cc_start: 0.9273 (tttp) cc_final: 0.8879 (tptm) REVERT: G 35 ASP cc_start: 0.8886 (m-30) cc_final: 0.8303 (m-30) REVERT: G 45 LYS cc_start: 0.9118 (mppt) cc_final: 0.8835 (tppt) REVERT: G 47 ASP cc_start: 0.8733 (t0) cc_final: 0.8322 (t0) outliers start: 47 outliers final: 28 residues processed: 229 average time/residue: 0.0738 time to fit residues: 24.5127 Evaluate side-chains 217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 266 VAL Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR 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 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 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 16 GLU 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: 6.9990 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 GLN R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089894 restraints weight = 16986.226| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.94 r_work: 0.3200 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6841 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= 0.130 Angle : 0.571 7.292 12415 Z= 0.292 Chirality : 0.042 0.162 1420 Planarity : 0.003 0.045 1551 Dihedral : 5.315 57.680 1424 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.47 % Allowed : 20.48 % 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: 0.01 (0.26), residues: 1110 helix: 2.07 (0.27), residues: 383 sheet: -1.18 (0.29), residues: 270 loop : -0.98 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 12 TYR 0.016 0.001 TYR R 199 PHE 0.031 0.001 PHE E 239 TRP 0.037 0.001 TRP L 21 HIS 0.006 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9145) covalent geometry : angle 0.57047 (12411) SS BOND : bond 0.00231 ( 2) SS BOND : angle 1.46352 ( 4) hydrogen bonds : bond 0.03180 ( 416) hydrogen bonds : angle 3.92856 ( 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 238 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8171 (tt) REVERT: R 97 ASP cc_start: 0.8397 (t70) cc_final: 0.7970 (t0) REVERT: R 205 LEU cc_start: 0.9236 (tp) cc_final: 0.8990 (tt) REVERT: R 212 MET cc_start: 0.8255 (tpp) cc_final: 0.7001 (ttt) REVERT: R 286 TYR cc_start: 0.8416 (t80) cc_final: 0.7913 (t80) REVERT: R 295 ASP cc_start: 0.8068 (p0) cc_final: 0.6993 (p0) REVERT: A 26 GLU cc_start: 0.8320 (tp30) cc_final: 0.7879 (tp30) REVERT: A 28 GLN cc_start: 0.8606 (tp40) cc_final: 0.8329 (tp40) REVERT: B 135 GLU cc_start: 0.8825 (mp0) cc_final: 0.8599 (mp0) REVERT: B 193 MET cc_start: 0.8336 (mmt) cc_final: 0.7946 (mmm) REVERT: B 203 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8818 (pp) REVERT: B 216 TRP cc_start: 0.8771 (m100) cc_final: 0.8341 (m100) REVERT: B 220 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: B 302 TRP cc_start: 0.9134 (m100) cc_final: 0.8500 (m-10) REVERT: B 334 THR cc_start: 0.9381 (m) cc_final: 0.9099 (p) REVERT: B 344 TRP cc_start: 0.8945 (m100) cc_final: 0.8572 (m-10) REVERT: E 42 LYS cc_start: 0.9275 (mmmm) cc_final: 0.9034 (mmmm) REVERT: E 79 PHE cc_start: 0.7904 (m-80) cc_final: 0.7690 (m-80) REVERT: E 90 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8271 (t) REVERT: E 165 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7912 (pp) REVERT: E 192 MET cc_start: 0.6971 (ptm) cc_final: 0.6223 (ppp) REVERT: G 12 ARG cc_start: 0.8712 (ptp90) cc_final: 0.8263 (ptp90) REVERT: G 13 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8505 (mmtm) REVERT: G 31 LYS cc_start: 0.9275 (tttp) cc_final: 0.8875 (tptm) REVERT: G 35 ASP cc_start: 0.8906 (m-30) cc_final: 0.8313 (m-30) REVERT: G 45 LYS cc_start: 0.9118 (mppt) cc_final: 0.8842 (tppt) REVERT: G 47 ASP cc_start: 0.8716 (t0) cc_final: 0.8304 (t0) outliers start: 43 outliers final: 30 residues processed: 221 average time/residue: 0.0788 time to fit residues: 24.8417 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 313 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 GLN 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 64 TYR Chi-restraints excluded: chain B residue 83 LYS 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 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 14 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: 0.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089592 restraints weight = 17049.701| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.93 r_work: 0.3184 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9147 Z= 0.140 Angle : 0.578 7.482 12415 Z= 0.298 Chirality : 0.042 0.162 1420 Planarity : 0.004 0.045 1551 Dihedral : 5.223 58.862 1424 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.78 % Allowed : 20.27 % 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: 0.09 (0.26), residues: 1110 helix: 2.11 (0.27), residues: 383 sheet: -1.09 (0.30), residues: 270 loop : -0.94 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 12 TYR 0.016 0.001 TYR R 199 PHE 0.026 0.001 PHE E 239 TRP 0.027 0.001 TRP L 21 HIS 0.006 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9145) covalent geometry : angle 0.57778 (12411) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.50104 ( 4) hydrogen bonds : bond 0.03252 ( 416) hydrogen bonds : angle 3.95016 ( 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 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8172 (tt) REVERT: R 97 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8019 (t0) REVERT: R 205 LEU cc_start: 0.9230 (tp) cc_final: 0.8991 (tt) REVERT: R 212 MET cc_start: 0.8316 (tpp) cc_final: 0.7032 (ttt) REVERT: R 286 TYR cc_start: 0.8443 (t80) cc_final: 0.7914 (t80) REVERT: R 295 ASP cc_start: 0.8101 (p0) cc_final: 0.7112 (p0) REVERT: R 298 MET cc_start: 0.8405 (mmt) cc_final: 0.8010 (tpp) REVERT: A 14 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: A 26 GLU cc_start: 0.8323 (tp30) cc_final: 0.7887 (tp30) REVERT: A 28 GLN cc_start: 0.8605 (tp40) cc_final: 0.8336 (tp40) REVERT: B 193 MET cc_start: 0.8372 (mmt) cc_final: 0.7976 (mmm) REVERT: B 203 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8827 (pp) REVERT: B 220 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: B 302 TRP cc_start: 0.9143 (m100) cc_final: 0.8517 (m-10) REVERT: B 334 THR cc_start: 0.9410 (m) cc_final: 0.9107 (p) REVERT: B 344 TRP cc_start: 0.8935 (m100) cc_final: 0.8568 (m-10) REVERT: E 42 LYS cc_start: 0.9294 (mmmm) cc_final: 0.9041 (mmmm) REVERT: E 45 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: E 90 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (t) REVERT: E 192 MET cc_start: 0.6944 (ptm) cc_final: 0.6023 (ppp) REVERT: E 229 CYS cc_start: 0.8843 (p) cc_final: 0.8513 (p) REVERT: G 13 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8565 (mmtm) REVERT: G 31 LYS cc_start: 0.9275 (tttp) cc_final: 0.8867 (tptm) REVERT: G 35 ASP cc_start: 0.8927 (m-30) cc_final: 0.8320 (m-30) REVERT: G 45 LYS cc_start: 0.9122 (mppt) cc_final: 0.8855 (tppt) REVERT: G 47 ASP cc_start: 0.8742 (t0) cc_final: 0.8315 (t0) outliers start: 46 outliers final: 33 residues processed: 220 average time/residue: 0.0769 time to fit residues: 24.4439 Evaluate side-chains 214 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS 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 299 LEU Chi-restraints excluded: chain R residue 313 THR 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 209 GLN 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 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 188 HIS 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 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 159 CYS Chi-restraints excluded: chain G residue 14 LEU 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: 0.0670 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 GLN R 280 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088467 restraints weight = 17090.657| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.91 r_work: 0.3171 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9147 Z= 0.152 Angle : 0.605 9.626 12415 Z= 0.312 Chirality : 0.043 0.171 1420 Planarity : 0.004 0.051 1551 Dihedral : 5.203 59.057 1424 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.78 % Allowed : 20.48 % Favored : 74.74 % 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: 0.10 (0.26), residues: 1110 helix: 2.08 (0.27), residues: 384 sheet: -0.97 (0.30), residues: 264 loop : -0.99 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR R 199 PHE 0.021 0.001 PHE E 239 TRP 0.024 0.001 TRP L 21 HIS 0.006 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9145) covalent geometry : angle 0.60418 (12411) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.59642 ( 4) hydrogen bonds : bond 0.03423 ( 416) hydrogen bonds : angle 3.98467 ( 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 228 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.294 Fit side-chains REVERT: R 61 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8156 (tt) REVERT: R 97 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8094 (t70) REVERT: R 205 LEU cc_start: 0.9228 (tp) cc_final: 0.8987 (tt) REVERT: R 212 MET cc_start: 0.8355 (tpp) cc_final: 0.7031 (ttt) REVERT: R 286 TYR cc_start: 0.8474 (t80) cc_final: 0.7928 (t80) REVERT: R 298 MET cc_start: 0.8406 (mmt) cc_final: 0.8044 (tpp) REVERT: A 14 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: A 26 GLU cc_start: 0.8364 (tp30) cc_final: 0.7912 (tp30) REVERT: A 28 GLN cc_start: 0.8614 (tp40) cc_final: 0.8330 (tp40) REVERT: B 193 MET cc_start: 0.8374 (mmt) cc_final: 0.7969 (mmm) REVERT: B 203 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (pp) REVERT: B 220 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: B 302 TRP cc_start: 0.9164 (m100) cc_final: 0.8491 (m-10) REVERT: B 334 THR cc_start: 0.9423 (m) cc_final: 0.9101 (p) REVERT: B 344 TRP cc_start: 0.8941 (m100) cc_final: 0.8574 (m-10) REVERT: E 42 LYS cc_start: 0.9294 (mmmm) cc_final: 0.9052 (mmmm) REVERT: E 45 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: E 90 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8224 (t) REVERT: E 179 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7474 (tm-30) REVERT: E 192 MET cc_start: 0.6886 (ptm) cc_final: 0.6053 (ppp) REVERT: E 229 CYS cc_start: 0.8881 (p) cc_final: 0.8562 (p) REVERT: G 12 ARG cc_start: 0.8672 (ptp90) cc_final: 0.8409 (ptp90) REVERT: G 13 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8658 (mmtm) REVERT: G 31 LYS cc_start: 0.9263 (tttp) cc_final: 0.8837 (tptm) REVERT: G 35 ASP cc_start: 0.8929 (m-30) cc_final: 0.8330 (m-30) REVERT: G 45 LYS cc_start: 0.9139 (mppt) cc_final: 0.8846 (tppt) REVERT: G 47 ASP cc_start: 0.8780 (t0) cc_final: 0.8395 (t0) outliers start: 46 outliers final: 31 residues processed: 213 average time/residue: 0.0743 time to fit residues: 22.9028 Evaluate side-chains 211 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 97 ASP 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 299 LEU Chi-restraints excluded: chain R residue 313 THR 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 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 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 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 159 CYS Chi-restraints excluded: chain G residue 16 GLU 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: 0.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.119412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089356 restraints weight = 16989.406| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.95 r_work: 0.3202 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9147 Z= 0.127 Angle : 0.608 10.873 12415 Z= 0.313 Chirality : 0.043 0.161 1420 Planarity : 0.004 0.055 1551 Dihedral : 5.122 57.466 1424 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.64 % Allowed : 21.83 % Favored : 74.53 % 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: 2.11 (0.27), residues: 384 sheet: -0.87 (0.30), residues: 263 loop : -0.97 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.014 0.001 TYR R 199 PHE 0.018 0.001 PHE E 239 TRP 0.024 0.001 TRP L 21 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9145) covalent geometry : angle 0.60731 (12411) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.44493 ( 4) hydrogen bonds : bond 0.03324 ( 416) hydrogen bonds : angle 3.94172 ( 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 221 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.308 Fit side-chains REVERT: R 61 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (tt) REVERT: R 97 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8070 (t70) REVERT: R 155 MET cc_start: 0.6017 (tpt) cc_final: 0.5613 (tpp) REVERT: R 205 LEU cc_start: 0.9210 (tp) cc_final: 0.8944 (tt) REVERT: R 212 MET cc_start: 0.8306 (tpp) cc_final: 0.6990 (ttt) REVERT: R 286 TYR cc_start: 0.8466 (t80) cc_final: 0.7944 (t80) REVERT: R 298 MET cc_start: 0.8384 (mmt) cc_final: 0.8017 (tpp) REVERT: A 26 GLU cc_start: 0.8310 (tp30) cc_final: 0.7862 (tp30) REVERT: A 28 GLN cc_start: 0.8566 (tp40) cc_final: 0.8294 (tp40) REVERT: A 59 MET cc_start: 0.8993 (ppp) cc_final: 0.8509 (ppp) REVERT: B 193 MET cc_start: 0.8297 (mmt) cc_final: 0.7916 (mmm) REVERT: B 203 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8793 (pp) REVERT: B 220 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: B 302 TRP cc_start: 0.9104 (m100) cc_final: 0.8523 (m-10) REVERT: B 334 THR cc_start: 0.9382 (m) cc_final: 0.9115 (p) REVERT: B 344 TRP cc_start: 0.8893 (m100) cc_final: 0.8557 (m-10) REVERT: E 42 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9008 (mmmm) REVERT: E 90 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8183 (t) REVERT: E 179 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 192 MET cc_start: 0.6639 (ptm) cc_final: 0.5410 (ppp) REVERT: E 229 CYS cc_start: 0.8804 (p) cc_final: 0.8527 (p) REVERT: G 12 ARG cc_start: 0.8658 (ptp90) cc_final: 0.8361 (ptp90) REVERT: G 13 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8675 (mmtm) REVERT: G 31 LYS cc_start: 0.9240 (tttp) cc_final: 0.8813 (tptm) REVERT: G 35 ASP cc_start: 0.8924 (m-30) cc_final: 0.8324 (m-30) REVERT: G 45 LYS cc_start: 0.9135 (mppt) cc_final: 0.8846 (tppt) REVERT: G 47 ASP cc_start: 0.8737 (t0) cc_final: 0.8307 (t0) outliers start: 35 outliers final: 26 residues processed: 207 average time/residue: 0.0747 time to fit residues: 22.2896 Evaluate side-chains 206 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 97 ASP 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 299 LEU Chi-restraints excluded: chain R residue 317 VAL 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 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 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU 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 G residue 16 GLU 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: 1.9990 chunk 94 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 62 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 GLN R 280 ASN R 314 ASN ** A 209 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 = 0.3821 r_free = 0.3821 target = 0.121431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091333 restraints weight = 16846.883| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.95 r_work: 0.3238 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9147 Z= 0.117 Angle : 0.619 11.760 12415 Z= 0.314 Chirality : 0.043 0.185 1420 Planarity : 0.004 0.061 1551 Dihedral : 5.038 55.616 1424 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.01 % Allowed : 22.87 % Favored : 74.12 % 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: 0.26 (0.26), residues: 1110 helix: 2.12 (0.27), residues: 384 sheet: -0.71 (0.31), residues: 261 loop : -0.93 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 37 TYR 0.013 0.001 TYR R 199 PHE 0.025 0.001 PHE E 239 TRP 0.023 0.001 TRP L 21 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9145) covalent geometry : angle 0.61855 (12411) SS BOND : bond 0.00083 ( 2) SS BOND : angle 1.32787 ( 4) hydrogen bonds : bond 0.03280 ( 416) hydrogen bonds : angle 3.89484 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.96 seconds wall clock time: 38 minutes 57.80 seconds (2337.80 seconds total)