Starting phenix.real_space_refine on Thu Jun 4 02:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmg_65187/06_2026/9vmg_65187.map" } resolution = 2.82 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= 0.007 sd= 0.030 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 65 5.16 5 C 6209 2.51 5 N 1702 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9818 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1874 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2569 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 964 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1780 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 9818 At special positions: 0 Unit cell: (83.2, 122.304, 132.288, 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 65 16.00 O 1842 8.00 N 1702 7.00 C 6209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 125 " - pdb=" SG CYS R 156 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.76 Conformation dependent library (CDL) restraints added in 387.5 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 16 sheets defined 35.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.313A pdb=" N LEU R 70 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 94 removed outlier: 3.755A pdb=" N MET R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.923A pdb=" N THR R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 156 Processing helix chain 'R' and resid 159 through 169 removed outlier: 4.160A pdb=" N LEU R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA R 166 " --> pdb=" O VAL R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.557A pdb=" N HIS R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 206 removed outlier: 3.703A pdb=" N PHE R 203 " --> pdb=" O ALA R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 232 removed outlier: 3.540A pdb=" N LEU R 211 " --> pdb=" O VAL R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 280 Proline residue: R 269 - end of helix removed outlier: 3.986A pdb=" N VAL R 273 " --> pdb=" O PRO R 269 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 302 Processing helix chain 'R' and resid 302 through 308 Processing helix chain 'R' and resid 311 through 322 removed outlier: 3.564A pdb=" N LEU R 322 " --> pdb=" O PHE R 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 35 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.764A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.595A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.600A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.501A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.885A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.534A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.945A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.664A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.633A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.791A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 6.212A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.365A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.986A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.558A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.424A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.514A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.702A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.924A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.602A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.832A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.514A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.554A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE S 212 " --> pdb=" O CYS S 159 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1290 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: 1.73 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2503 1.33 - 1.46: 3035 1.46 - 1.59: 4392 1.59 - 1.72: 0 1.72 - 1.86: 92 Bond restraints: 10022 Sorted by residual: bond pdb=" N ILE R 85 " pdb=" CA ILE R 85 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.59e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.535 1.474 0.061 1.71e-02 3.42e+03 1.28e+01 bond pdb=" N LYS S 76 " pdb=" CA LYS S 76 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N VAL A 57 " pdb=" CA VAL A 57 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.22e-02 6.72e+03 9.45e+00 bond pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.10e-02 8.26e+03 9.11e+00 ... (remaining 10017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 13027 1.79 - 3.58: 490 3.58 - 5.37: 73 5.37 - 7.16: 8 7.16 - 8.95: 4 Bond angle restraints: 13602 Sorted by residual: angle pdb=" N TRP R 171 " pdb=" CA TRP R 171 " pdb=" C TRP R 171 " ideal model delta sigma weight residual 113.17 105.42 7.75 1.26e+00 6.30e-01 3.78e+01 angle pdb=" N ASP S 74 " pdb=" CA ASP S 74 " pdb=" C ASP S 74 " ideal model delta sigma weight residual 113.25 106.06 7.19 1.30e+00 5.92e-01 3.06e+01 angle pdb=" N PRO S 75 " pdb=" CA PRO S 75 " pdb=" C PRO S 75 " ideal model delta sigma weight residual 111.19 103.58 7.61 1.57e+00 4.06e-01 2.35e+01 angle pdb=" CA PRO S 75 " pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 121.31 116.27 5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" N MET R 169 " pdb=" CA MET R 169 " pdb=" C MET R 169 " ideal model delta sigma weight residual 113.19 108.54 4.65 1.19e+00 7.06e-01 1.53e+01 ... (remaining 13597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5395 17.10 - 34.20: 436 34.20 - 51.30: 80 51.30 - 68.39: 30 68.39 - 85.49: 6 Dihedral angle restraints: 5947 sinusoidal: 2263 harmonic: 3684 Sorted by residual: dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CD ARG R 218 " pdb=" NE ARG R 218 " pdb=" CZ ARG R 218 " pdb=" NH1 ARG R 218 " ideal model delta sinusoidal sigma weight residual 0.00 -32.71 32.71 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" SG CYS N 99 " pdb=" CB CYS N 107 " pdb=" SG CYS N 107 " pdb=" CA CYS N 107 " ideal model delta sinusoidal sigma weight residual 79.00 12.97 66.03 1 2.00e+01 2.50e-03 1.43e+01 ... (remaining 5944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1130 0.046 - 0.092: 293 0.092 - 0.138: 102 0.138 - 0.184: 15 0.184 - 0.230: 6 Chirality restraints: 1546 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU R 249 " pdb=" N GLU R 249 " pdb=" C GLU R 249 " pdb=" CB GLU R 249 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL N 126 " pdb=" N VAL N 126 " pdb=" C VAL N 126 " pdb=" CB VAL N 126 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1543 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 218 " 0.577 9.50e-02 1.11e+02 2.59e-01 4.09e+01 pdb=" NE ARG R 218 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG R 218 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG R 218 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG R 218 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 72 " -0.457 9.50e-02 1.11e+02 2.05e-01 2.58e+01 pdb=" NE ARG S 72 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG S 72 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG S 72 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG S 72 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 139 " 0.343 9.50e-02 1.11e+02 1.54e-01 1.45e+01 pdb=" NE ARG R 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG R 139 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 139 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 139 " 0.012 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1680 2.77 - 3.30: 9788 3.30 - 3.83: 17128 3.83 - 4.37: 20676 4.37 - 4.90: 35590 Nonbonded interactions: 84862 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.280 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.287 3.040 ... (remaining 84857 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: 1.840 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.970 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:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10027 Z= 0.303 Angle : 0.753 8.946 13612 Z= 0.492 Chirality : 0.049 0.230 1546 Planarity : 0.012 0.259 1735 Dihedral : 13.533 85.492 3556 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.29 % Allowed : 1.71 % Favored : 98.00 % 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: -0.38 (0.24), residues: 1252 helix: 0.94 (0.27), residues: 393 sheet: -0.87 (0.29), residues: 309 loop : -0.64 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 72 TYR 0.015 0.001 TYR N 60 PHE 0.011 0.001 PHE R 167 TRP 0.031 0.002 TRP R 294 HIS 0.005 0.001 HIS R 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.30 (10022) covalent geometry : angle 0.75042 / 0.49 (13602) SS BOND : bond 0.00685 / 0.35 ( 5) SS BOND : angle 2.54073 / 1.57 ( 10) hydrogen bonds : bond 0.18657 / 12.56 ( 457) hydrogen bonds : angle 7.93983 / 5.88 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7036 (t80) cc_final: 0.6669 (t80) REVERT: A 159 LYS cc_start: 0.8368 (mmpt) cc_final: 0.8138 (mmmt) REVERT: B 130 GLU cc_start: 0.7877 (mp0) cc_final: 0.7330 (mp0) REVERT: N 108 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6864 (t80) REVERT: S 138 ILE cc_start: 0.7978 (mt) cc_final: 0.7667 (mt) REVERT: S 183 GLN cc_start: 0.7647 (mt0) cc_final: 0.7051 (mm-40) REVERT: S 230 MET cc_start: 0.7996 (ttp) cc_final: 0.7346 (ttp) REVERT: S 231 GLN cc_start: 0.8574 (pp30) cc_final: 0.8236 (pt0) outliers start: 3 outliers final: 1 residues processed: 189 average time/residue: 0.5653 time to fit residues: 114.9285 Evaluate side-chains 166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN B 156 GLN B 220 GLN B 237 ASN N 31 ASN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.140083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113893 restraints weight = 15631.936| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.38 r_work: 0.3608 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10027 Z= 0.147 Angle : 0.580 13.845 13612 Z= 0.304 Chirality : 0.043 0.149 1546 Planarity : 0.005 0.041 1735 Dihedral : 4.855 55.100 1400 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 10.57 % Favored : 87.81 % 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: -0.11 (0.24), residues: 1252 helix: 1.48 (0.27), residues: 386 sheet: -0.66 (0.30), residues: 301 loop : -0.77 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 151 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE B 199 TRP 0.020 0.001 TRP R 294 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10022) covalent geometry : angle 0.57799 / 0.30 (13602) SS BOND : bond 0.00270 / 0.14 ( 5) SS BOND : angle 1.92382 / 1.05 ( 10) hydrogen bonds : bond 0.04176 / 2.77 ( 457) hydrogen bonds : angle 5.48460 / 4.03 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7555 (t80) cc_final: 0.7236 (t80) REVERT: A 147 ASP cc_start: 0.7623 (t70) cc_final: 0.7350 (p0) REVERT: A 228 PHE cc_start: 0.7492 (t80) cc_final: 0.7272 (t80) REVERT: B 130 GLU cc_start: 0.8132 (mp0) cc_final: 0.7425 (mp0) REVERT: B 138 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: B 262 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7769 (ttm) REVERT: N 108 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7118 (t80) REVERT: S 34 MET cc_start: 0.7561 (mmt) cc_final: 0.7260 (mmt) REVERT: S 138 ILE cc_start: 0.7975 (mt) cc_final: 0.7750 (mt) REVERT: S 183 GLN cc_start: 0.8048 (mt0) cc_final: 0.7163 (mm-40) REVERT: S 227 TYR cc_start: 0.8038 (m-80) cc_final: 0.7828 (m-80) outliers start: 17 outliers final: 5 residues processed: 175 average time/residue: 0.5635 time to fit residues: 106.1475 Evaluate side-chains 166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN B 220 GLN B 237 ASN N 31 ASN N 84 ASN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.139021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112685 restraints weight = 15577.328| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.38 r_work: 0.3576 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10027 Z= 0.171 Angle : 0.566 7.455 13612 Z= 0.297 Chirality : 0.043 0.153 1546 Planarity : 0.004 0.040 1735 Dihedral : 4.782 52.938 1398 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.38 % Allowed : 13.14 % Favored : 84.48 % 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: -0.12 (0.24), residues: 1252 helix: 1.50 (0.27), residues: 387 sheet: -0.71 (0.29), residues: 309 loop : -0.77 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 151 TYR 0.018 0.001 TYR S 190 PHE 0.014 0.001 PHE B 151 TRP 0.019 0.002 TRP R 294 HIS 0.012 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (10022) covalent geometry : angle 0.56314 / 0.30 (13602) SS BOND : bond 0.00297 / 0.15 ( 5) SS BOND : angle 2.00112 / 1.10 ( 10) hydrogen bonds : bond 0.03960 / 2.59 ( 457) hydrogen bonds : angle 5.19278 / 3.82 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7553 (t80) cc_final: 0.7265 (t80) REVERT: A 151 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6738 (mm-30) REVERT: A 228 PHE cc_start: 0.7533 (t80) cc_final: 0.7307 (t80) REVERT: B 130 GLU cc_start: 0.8108 (mp0) cc_final: 0.7318 (mp0) REVERT: B 262 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7925 (ttm) REVERT: N 3 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: N 108 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7073 (t80) REVERT: S 138 ILE cc_start: 0.7979 (mt) cc_final: 0.7778 (mt) REVERT: S 183 GLN cc_start: 0.8022 (mt0) cc_final: 0.7206 (mm-40) outliers start: 25 outliers final: 8 residues processed: 182 average time/residue: 0.5387 time to fit residues: 105.8228 Evaluate side-chains 165 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 105 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN N 31 ASN N 84 ASN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115773 restraints weight = 15748.268| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.35 r_work: 0.3628 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10027 Z= 0.117 Angle : 0.538 9.533 13612 Z= 0.280 Chirality : 0.042 0.330 1546 Planarity : 0.004 0.056 1735 Dihedral : 4.642 53.650 1398 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.29 % Allowed : 16.38 % Favored : 81.33 % 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: -0.02 (0.24), residues: 1252 helix: 1.65 (0.27), residues: 381 sheet: -0.53 (0.30), residues: 301 loop : -0.81 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 46 TYR 0.012 0.001 TYR N 60 PHE 0.016 0.001 PHE S 80 TRP 0.021 0.001 TRP R 294 HIS 0.011 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10022) covalent geometry : angle 0.53644 / 0.28 (13602) SS BOND : bond 0.00269 / 0.13 ( 5) SS BOND : angle 1.73354 / 0.99 ( 10) hydrogen bonds : bond 0.03537 / 2.33 ( 457) hydrogen bonds : angle 4.94814 / 3.62 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7560 (t80) cc_final: 0.7008 (t80) REVERT: A 151 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 208 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7856 (mtt90) REVERT: B 130 GLU cc_start: 0.8103 (mp0) cc_final: 0.7345 (mp0) REVERT: B 262 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: N 3 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: N 108 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7157 (t80) REVERT: S 21 SER cc_start: 0.8054 (p) cc_final: 0.7778 (t) REVERT: S 183 GLN cc_start: 0.7911 (mt0) cc_final: 0.7099 (mm-40) outliers start: 24 outliers final: 5 residues processed: 177 average time/residue: 0.5195 time to fit residues: 99.3393 Evaluate side-chains 158 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 112 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 121 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 311 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN N 84 ASN S 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115818 restraints weight = 15681.346| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.34 r_work: 0.3627 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10027 Z= 0.119 Angle : 0.539 12.663 13612 Z= 0.277 Chirality : 0.041 0.145 1546 Planarity : 0.004 0.041 1735 Dihedral : 4.570 53.867 1398 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 18.19 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1252 helix: 1.69 (0.27), residues: 382 sheet: -0.56 (0.30), residues: 306 loop : -0.75 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 87 TYR 0.013 0.001 TYR N 95 PHE 0.016 0.001 PHE R 280 TRP 0.021 0.001 TRP R 294 HIS 0.012 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10022) covalent geometry : angle 0.53696 / 0.28 (13602) SS BOND : bond 0.00247 / 0.12 ( 5) SS BOND : angle 1.64870 / 0.96 ( 10) hydrogen bonds : bond 0.03438 / 2.26 ( 457) hydrogen bonds : angle 4.81421 / 3.53 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 256 MET cc_start: 0.7581 (mmp) cc_final: 0.7361 (tpt) REVERT: A 31 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7666 (tp30) REVERT: A 70 PHE cc_start: 0.7480 (t80) cc_final: 0.6922 (t80) REVERT: A 151 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 228 PHE cc_start: 0.7438 (t80) cc_final: 0.7212 (t80) REVERT: B 262 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7723 (ttm) REVERT: N 108 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7187 (t80) REVERT: S 21 SER cc_start: 0.8034 (p) cc_final: 0.7765 (t) REVERT: S 87 ARG cc_start: 0.7893 (ptp90) cc_final: 0.7638 (ptp90) REVERT: S 183 GLN cc_start: 0.7781 (mt0) cc_final: 0.7001 (mm-40) REVERT: S 230 MET cc_start: 0.8141 (ttp) cc_final: 0.7758 (ttp) outliers start: 25 outliers final: 9 residues processed: 173 average time/residue: 0.5478 time to fit residues: 102.2563 Evaluate side-chains 159 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 311 ASN B 220 GLN B 237 ASN N 31 ASN N 84 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.134790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108678 restraints weight = 15893.102| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.32 r_work: 0.3527 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10027 Z= 0.285 Angle : 0.676 12.489 13612 Z= 0.349 Chirality : 0.047 0.307 1546 Planarity : 0.005 0.050 1735 Dihedral : 5.253 52.842 1398 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.67 % Allowed : 19.05 % Favored : 78.29 % 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: -0.29 (0.24), residues: 1252 helix: 1.25 (0.26), residues: 379 sheet: -0.65 (0.29), residues: 300 loop : -0.86 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 46 TYR 0.029 0.002 TYR S 190 PHE 0.016 0.002 PHE B 151 TRP 0.021 0.002 TRP R 289 HIS 0.013 0.002 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.28 (10022) covalent geometry : angle 0.67317 / 0.35 (13602) SS BOND : bond 0.00328 / 0.17 ( 5) SS BOND : angle 2.38340 / 1.28 ( 10) hydrogen bonds : bond 0.04347 / 2.85 ( 457) hydrogen bonds : angle 5.26965 / 3.90 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 171 TRP cc_start: 0.7673 (m100) cc_final: 0.7017 (m-10) REVERT: R 266 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 70 PHE cc_start: 0.7568 (t80) cc_final: 0.7266 (t80) REVERT: A 151 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6810 (mm-30) REVERT: A 208 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7472 (mtm110) REVERT: N 12 VAL cc_start: 0.7237 (m) cc_final: 0.7030 (p) REVERT: N 76 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8234 (mtpp) REVERT: N 108 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7130 (t80) REVERT: S 21 SER cc_start: 0.8093 (p) cc_final: 0.7719 (t) REVERT: S 87 ARG cc_start: 0.7839 (ptp90) cc_final: 0.7574 (ptp90) REVERT: S 138 ILE cc_start: 0.8046 (mt) cc_final: 0.7807 (mt) REVERT: S 183 GLN cc_start: 0.7832 (mt0) cc_final: 0.7007 (mm-40) REVERT: S 230 MET cc_start: 0.8248 (ttp) cc_final: 0.7854 (ttp) outliers start: 28 outliers final: 12 residues processed: 170 average time/residue: 0.5374 time to fit residues: 98.5731 Evaluate side-chains 157 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 HIS ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN N 84 ASN S 82 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.138308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112520 restraints weight = 15628.786| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.31 r_work: 0.3585 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10027 Z= 0.146 Angle : 0.595 10.262 13612 Z= 0.306 Chirality : 0.043 0.154 1546 Planarity : 0.004 0.041 1735 Dihedral : 4.988 54.133 1398 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.48 % Allowed : 20.19 % Favored : 77.33 % 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: -0.16 (0.24), residues: 1252 helix: 1.44 (0.26), residues: 385 sheet: -0.54 (0.29), residues: 301 loop : -0.89 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.016 0.001 TYR S 59 PHE 0.017 0.002 PHE R 280 TRP 0.032 0.002 TRP R 294 HIS 0.012 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10022) covalent geometry : angle 0.59258 / 0.30 (13602) SS BOND : bond 0.00333 / 0.16 ( 5) SS BOND : angle 2.24538 / 1.17 ( 10) hydrogen bonds : bond 0.03731 / 2.44 ( 457) hydrogen bonds : angle 4.99005 / 3.67 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 171 TRP cc_start: 0.7657 (m100) cc_final: 0.7014 (m-10) REVERT: R 229 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7455 (ttpp) REVERT: R 266 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 70 PHE cc_start: 0.7518 (t80) cc_final: 0.6953 (t80) REVERT: A 151 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 228 PHE cc_start: 0.7437 (t80) cc_final: 0.7206 (t80) REVERT: N 104 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8218 (m) REVERT: N 108 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7037 (t80) REVERT: S 21 SER cc_start: 0.8051 (p) cc_final: 0.7769 (t) REVERT: S 87 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7596 (ptp90) REVERT: S 138 ILE cc_start: 0.8048 (mt) cc_final: 0.7821 (mt) REVERT: S 183 GLN cc_start: 0.7707 (mt0) cc_final: 0.6893 (mm-40) REVERT: S 230 MET cc_start: 0.8113 (ttp) cc_final: 0.7641 (ttp) outliers start: 26 outliers final: 13 residues processed: 168 average time/residue: 0.5414 time to fit residues: 98.1695 Evaluate side-chains 162 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 229 LYS Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 106 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN B 340 ASN S 82 GLN S 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.118659 restraints weight = 15764.751| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.35 r_work: 0.3599 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10027 Z= 0.131 Angle : 0.594 13.479 13612 Z= 0.300 Chirality : 0.043 0.320 1546 Planarity : 0.004 0.038 1735 Dihedral : 4.853 54.939 1398 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 21.14 % Favored : 76.67 % 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 (0.24), residues: 1252 helix: 1.49 (0.26), residues: 387 sheet: -0.56 (0.29), residues: 304 loop : -0.84 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.014 0.001 TYR N 95 PHE 0.012 0.001 PHE B 151 TRP 0.037 0.001 TRP R 294 HIS 0.012 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10022) covalent geometry : angle 0.59183 / 0.30 (13602) SS BOND : bond 0.00291 / 0.14 ( 5) SS BOND : angle 2.00166 / 1.08 ( 10) hydrogen bonds : bond 0.03558 / 2.35 ( 457) hydrogen bonds : angle 4.88241 / 3.59 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 171 TRP cc_start: 0.7646 (m100) cc_final: 0.6978 (m-10) REVERT: R 229 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7410 (ttpp) REVERT: R 280 PHE cc_start: 0.7525 (p90) cc_final: 0.7197 (p90) REVERT: A 70 PHE cc_start: 0.7510 (t80) cc_final: 0.6958 (t80) REVERT: A 151 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6759 (mm-30) REVERT: A 228 PHE cc_start: 0.7492 (t80) cc_final: 0.7247 (t80) REVERT: N 104 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8165 (m) REVERT: N 108 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7092 (t80) REVERT: S 21 SER cc_start: 0.8025 (p) cc_final: 0.7754 (t) REVERT: S 87 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7580 (ptp90) REVERT: S 138 ILE cc_start: 0.8020 (mt) cc_final: 0.7786 (mt) REVERT: S 183 GLN cc_start: 0.7563 (mt0) cc_final: 0.6796 (mm-40) REVERT: S 230 MET cc_start: 0.8082 (ttp) cc_final: 0.7736 (ttp) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.5156 time to fit residues: 92.6550 Evaluate side-chains 165 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 229 LYS Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN B 156 GLN B 220 GLN B 237 ASN N 84 ASN S 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119369 restraints weight = 15671.590| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.32 r_work: 0.3607 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10027 Z= 0.132 Angle : 0.606 15.976 13612 Z= 0.302 Chirality : 0.043 0.247 1546 Planarity : 0.004 0.037 1735 Dihedral : 4.846 55.700 1398 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.19 % Allowed : 21.71 % Favored : 76.10 % 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: -0.06 (0.24), residues: 1252 helix: 1.50 (0.26), residues: 391 sheet: -0.53 (0.29), residues: 304 loop : -0.81 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 87 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.001 PHE B 151 TRP 0.036 0.002 TRP R 294 HIS 0.013 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10022) covalent geometry : angle 0.60439 / 0.30 (13602) SS BOND : bond 0.00241 / 0.12 ( 5) SS BOND : angle 1.95556 / 1.06 ( 10) hydrogen bonds : bond 0.03509 / 2.31 ( 457) hydrogen bonds : angle 4.81019 / 3.54 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 171 TRP cc_start: 0.7618 (m100) cc_final: 0.7004 (m-10) REVERT: R 229 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7403 (ttpp) REVERT: R 280 PHE cc_start: 0.7489 (p90) cc_final: 0.7186 (p90) REVERT: A 16 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7352 (tttm) REVERT: A 31 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7664 (tp30) REVERT: A 70 PHE cc_start: 0.7492 (t80) cc_final: 0.6947 (t80) REVERT: A 151 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6731 (mm-30) REVERT: A 208 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.8002 (mtm180) REVERT: A 228 PHE cc_start: 0.7460 (t80) cc_final: 0.7199 (t80) REVERT: N 104 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8010 (p) REVERT: N 108 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7239 (t80) REVERT: S 21 SER cc_start: 0.8031 (p) cc_final: 0.7788 (t) REVERT: S 87 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7575 (ptp90) REVERT: S 138 ILE cc_start: 0.8039 (mt) cc_final: 0.7811 (mt) REVERT: S 183 GLN cc_start: 0.7444 (mt0) cc_final: 0.6708 (mm-40) REVERT: S 230 MET cc_start: 0.8127 (ttp) cc_final: 0.7701 (ttp) outliers start: 23 outliers final: 13 residues processed: 166 average time/residue: 0.5203 time to fit residues: 93.2863 Evaluate side-chains 164 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 229 LYS Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.0040 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN B 220 GLN B 237 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.147127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.121890 restraints weight = 15422.586| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.29 r_work: 0.3610 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10027 Z= 0.132 Angle : 0.608 14.843 13612 Z= 0.301 Chirality : 0.042 0.216 1546 Planarity : 0.005 0.100 1735 Dihedral : 4.868 55.763 1398 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 22.00 % Favored : 75.81 % 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: -0.06 (0.24), residues: 1252 helix: 1.51 (0.26), residues: 390 sheet: -0.55 (0.29), residues: 306 loop : -0.80 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 46 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.001 PHE B 151 TRP 0.037 0.001 TRP R 294 HIS 0.013 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10022) covalent geometry : angle 0.60557 / 0.30 (13602) SS BOND : bond 0.00232 / 0.12 ( 5) SS BOND : angle 1.89667 / 1.03 ( 10) hydrogen bonds : bond 0.03468 / 2.29 ( 457) hydrogen bonds : angle 4.79127 / 3.53 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 171 TRP cc_start: 0.7591 (m100) cc_final: 0.6991 (m-10) REVERT: R 280 PHE cc_start: 0.7461 (p90) cc_final: 0.7165 (p90) REVERT: A 16 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7377 (tttm) REVERT: A 31 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7687 (tp30) REVERT: A 70 PHE cc_start: 0.7524 (t80) cc_final: 0.7001 (t80) REVERT: A 151 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6739 (mm-30) REVERT: A 208 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: A 228 PHE cc_start: 0.7400 (t80) cc_final: 0.7152 (t80) REVERT: N 104 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8072 (p) REVERT: N 108 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7109 (t80) REVERT: S 21 SER cc_start: 0.8017 (p) cc_final: 0.7798 (t) REVERT: S 87 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7574 (ptp90) REVERT: S 138 ILE cc_start: 0.8070 (mt) cc_final: 0.7837 (mt) REVERT: S 183 GLN cc_start: 0.7355 (mt0) cc_final: 0.6674 (mm-40) REVERT: S 230 MET cc_start: 0.8105 (ttp) cc_final: 0.7744 (ttp) outliers start: 23 outliers final: 16 residues processed: 163 average time/residue: 0.5111 time to fit residues: 89.9745 Evaluate side-chains 164 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 102 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN B 220 GLN B 237 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.147314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122153 restraints weight = 15630.334| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.31 r_work: 0.3612 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10027 Z= 0.128 Angle : 0.593 13.974 13612 Z= 0.297 Chirality : 0.042 0.190 1546 Planarity : 0.004 0.084 1735 Dihedral : 4.796 56.212 1398 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.29 % Allowed : 21.90 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1252 helix: 1.55 (0.26), residues: 392 sheet: -0.57 (0.30), residues: 307 loop : -0.78 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 46 TYR 0.013 0.001 TYR N 95 PHE 0.011 0.001 PHE B 151 TRP 0.037 0.001 TRP R 294 HIS 0.012 0.001 HIS R 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10022) covalent geometry : angle 0.59131 / 0.30 (13602) SS BOND : bond 0.00230 / 0.11 ( 5) SS BOND : angle 1.83824 / 1.01 ( 10) hydrogen bonds : bond 0.03411 / 2.25 ( 457) hydrogen bonds : angle 4.71902 / 3.47 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.42 seconds wall clock time: 78 minutes 14.10 seconds (4694.10 seconds total)