Starting phenix.real_space_refine on Thu Jun 4 04:06:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033.map" model { file = "/net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izh_61033/06_2026/9izh_61033_neut.cif" } resolution = 3.04 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= -0.003 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2192 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 66 5.16 5 C 5647 2.51 5 N 1517 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 8861 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2362 Classifications: {'peptide': 299} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1685 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2603 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} 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: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 448 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} 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: "S" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1734 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8861 At special positions: 0 Unit cell: (93.06, 115.83, 134.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 1 15.00 O 1630 8.00 N 1517 7.00 C 5647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " 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: 0.77 Conformation dependent library (CDL) restraints added in 251.4 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 36.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 29 through 37 removed outlier: 4.292A pdb=" N PHE R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 36 " --> pdb=" O PHE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 removed outlier: 3.504A pdb=" N THR R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU R 68 " --> pdb=" O MET R 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 81 removed outlier: 3.848A pdb=" N HIS R 81 " --> pdb=" O ARG R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 81' Processing helix chain 'R' and resid 82 through 108 removed outlier: 3.560A pdb=" N LEU R 87 " --> pdb=" O PRO R 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 105 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 107 " --> pdb=" O PHE R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 149 removed outlier: 3.958A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA R 134 " --> pdb=" O THR R 130 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 159 removed outlier: 3.509A pdb=" N MET R 159 " --> pdb=" O HIS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 removed outlier: 3.772A pdb=" N VAL R 165 " --> pdb=" O ASN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 184 No H-bonds generated for 'chain 'R' and resid 182 through 184' Processing helix chain 'R' and resid 203 through 239 removed outlier: 3.664A pdb=" N LEU R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL R 208 " --> pdb=" O ASP R 204 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN R 234 " --> pdb=" O GLY R 230 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 256 removed outlier: 3.720A pdb=" N MET R 253 " --> pdb=" O ASN R 249 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER R 255 " --> pdb=" O ASP R 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 256 " --> pdb=" O THR R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 284 removed outlier: 3.825A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.523A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 302 removed outlier: 3.534A pdb=" N LEU R 297 " --> pdb=" O GLU R 293 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 307 Processing helix chain 'R' and resid 315 through 326 Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.566A pdb=" N ALA A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 26 " --> pdb=" O CYS A 22 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.929A pdb=" N ARG A 90 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.439A pdb=" N THR A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.940A pdb=" N GLU A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.574A pdb=" N ILE A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.593A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.524A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.687A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.577A pdb=" N VAL A 34 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 84 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 36 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 35 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU A 107 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A 37 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 39 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 139 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N HIS A 198 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A 141 " --> pdb=" O HIS A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.587A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.844A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.386A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.595A 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 153 removed outlier: 6.352A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.742A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.556A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.181A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.100A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.384A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.539A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135 removed outlier: 4.177A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1119 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: 1.36 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1485 1.32 - 1.45: 2449 1.45 - 1.57: 5006 1.57 - 1.69: 1 1.69 - 1.81: 101 Bond restraints: 9042 Sorted by residual: bond pdb=" OAD NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.696 1.510 0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.683 1.513 0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" CAK NKP R 601 " pdb=" OAJ NKP R 601 " ideal model delta sigma weight residual 1.380 1.331 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.472 1.513 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" CAH NKP R 601 " pdb=" OBC NKP R 601 " ideal model delta sigma weight residual 1.468 1.430 0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 9037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.98: 12254 11.98 - 23.96: 1 23.96 - 35.94: 0 35.94 - 47.92: 0 47.92 - 59.90: 1 Bond angle restraints: 12256 Sorted by residual: angle pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAD NKP R 601 " ideal model delta sigma weight residual 53.21 113.11 -59.90 3.00e+00 1.11e-01 3.99e+02 angle pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAB NKP R 601 " ideal model delta sigma weight residual 128.27 112.63 15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" CA LYS A 225 " pdb=" CB LYS A 225 " pdb=" CG LYS A 225 " ideal model delta sigma weight residual 114.10 121.01 -6.91 2.00e+00 2.50e-01 1.19e+01 angle pdb=" N ALA A 202 " pdb=" CA ALA A 202 " pdb=" C ALA A 202 " ideal model delta sigma weight residual 112.97 109.60 3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAD NKP R 601 " ideal model delta sigma weight residual 121.86 112.89 8.97 3.00e+00 1.11e-01 8.93e+00 ... (remaining 12251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4585 17.97 - 35.94: 591 35.94 - 53.90: 154 53.90 - 71.87: 30 71.87 - 89.84: 7 Dihedral angle restraints: 5367 sinusoidal: 2051 harmonic: 3316 Sorted by residual: dihedral pdb=" CB CYS R 188 " pdb=" SG CYS R 188 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual 93.00 31.39 61.61 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1346 0.094 - 0.189: 59 0.189 - 0.283: 0 0.283 - 0.378: 0 0.378 - 0.472: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CAH NKP R 601 " pdb=" CAG NKP R 601 " pdb=" CAI NKP R 601 " pdb=" OBC NKP R 601 " both_signs ideal model delta sigma weight residual False -2.84 -2.37 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA ILE R 181 " pdb=" N ILE R 181 " pdb=" C ILE R 181 " pdb=" CB ILE R 181 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1403 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO S 224 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 236 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C THR B 196 " 0.032 2.00e-02 2.50e+03 pdb=" O THR B 196 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG B 197 " -0.011 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 142 2.67 - 3.22: 7831 3.22 - 3.78: 12873 3.78 - 4.34: 18597 4.34 - 4.90: 31681 Nonbonded interactions: 71124 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.108 3.040 nonbonded pdb=" O GLU A 126 " pdb=" ND2 ASN A 130 " model vdw 2.281 3.120 nonbonded pdb=" O SER S 105 " pdb=" NH2 ARG S 179 " model vdw 2.302 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.317 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.321 3.040 ... (remaining 71119 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.790 Find NCS groups from input model: 0.040 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.003 0.186 9044 Z= 0.170 Angle : 0.761 59.899 12260 Z= 0.329 Chirality : 0.041 0.472 1406 Planarity : 0.004 0.056 1547 Dihedral : 17.281 89.840 3219 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.32 % Allowed : 26.43 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1127 helix: -0.95 (0.25), residues: 383 sheet: -0.24 (0.32), residues: 274 loop : -0.99 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 114 TYR 0.028 0.001 TYR S 223 PHE 0.008 0.001 PHE B 199 TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 9042) covalent geometry : angle 0.76037 / 0.33 (12256) SS BOND : bond 0.00158 / 0.08 ( 2) SS BOND : angle 1.54717 / 0.88 ( 4) hydrogen bonds : bond 0.27702 / 18.04 ( 387) hydrogen bonds : angle 8.20598 / 5.81 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.340 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.1301 time to fit residues: 22.1265 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain B residue 267 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 125 GLN R 154 GLN R 194 ASN R 214 ASN A 43 ASN A 70 HIS A 89 GLN A 144 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 266 HIS S 35 HIS S 159 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.195968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161991 restraints weight = 9194.342| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.73 r_work: 0.3505 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9044 Z= 0.122 Angle : 0.535 7.049 12260 Z= 0.285 Chirality : 0.042 0.185 1406 Planarity : 0.005 0.063 1547 Dihedral : 5.955 55.015 1266 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.90 % Allowed : 24.42 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1127 helix: 0.77 (0.27), residues: 378 sheet: -0.17 (0.31), residues: 284 loop : -0.84 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 114 TYR 0.026 0.001 TYR S 223 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP S 47 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9042) covalent geometry : angle 0.53395 / 0.29 (12256) SS BOND : bond 0.00092 / 0.04 ( 2) SS BOND : angle 1.65587 / 0.94 ( 4) hydrogen bonds : bond 0.06210 / 4.14 ( 387) hydrogen bonds : angle 4.95197 / 3.47 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.396 Fit side-chains REVERT: A 126 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 130 ASN cc_start: 0.8172 (m-40) cc_final: 0.7861 (m110) REVERT: B 198 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8470 (mt) REVERT: C 21 MET cc_start: 0.7140 (mtp) cc_final: 0.6849 (ttt) REVERT: S 223 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6253 (t80) outliers start: 18 outliers final: 9 residues processed: 150 average time/residue: 0.1273 time to fit residues: 24.6364 Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN A 70 HIS ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.187692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154065 restraints weight = 9202.754| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.82 r_work: 0.3449 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9044 Z= 0.200 Angle : 0.611 8.885 12260 Z= 0.320 Chirality : 0.046 0.292 1406 Planarity : 0.005 0.059 1547 Dihedral : 5.959 55.581 1262 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.91 % Allowed : 23.15 % Favored : 72.94 % 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: -0.25 (0.25), residues: 1127 helix: 0.85 (0.27), residues: 384 sheet: -0.20 (0.31), residues: 280 loop : -0.93 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 114 TYR 0.030 0.002 TYR S 223 PHE 0.015 0.002 PHE B 151 TRP 0.012 0.002 TRP R 121 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 9042) covalent geometry : angle 0.61004 / 0.32 (12256) SS BOND : bond 0.00181 / 0.09 ( 2) SS BOND : angle 2.16372 / 1.24 ( 4) hydrogen bonds : bond 0.06786 / 4.53 ( 387) hydrogen bonds : angle 4.88813 / 3.42 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 88 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7865 (mtt) REVERT: A 126 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 43 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 267 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7871 (t0) REVERT: C 21 MET cc_start: 0.7115 (mtp) cc_final: 0.6718 (ttt) REVERT: S 223 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6524 (t80) outliers start: 37 outliers final: 23 residues processed: 157 average time/residue: 0.1221 time to fit residues: 24.8062 Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** A 230 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 = 0.4199 r_free = 0.4199 target = 0.196100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162424 restraints weight = 9182.025| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.80 r_work: 0.3539 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9044 Z= 0.099 Angle : 0.479 5.625 12260 Z= 0.257 Chirality : 0.041 0.268 1406 Planarity : 0.004 0.061 1547 Dihedral : 5.392 58.655 1262 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.22 % Allowed : 24.52 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1127 helix: 1.49 (0.27), residues: 380 sheet: -0.02 (0.31), residues: 283 loop : -0.79 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 114 TYR 0.021 0.001 TYR S 223 PHE 0.011 0.001 PHE B 199 TRP 0.010 0.001 TRP B 211 HIS 0.013 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 ( 9042) covalent geometry : angle 0.47818 / 0.26 (12256) SS BOND : bond 0.00187 / 0.10 ( 2) SS BOND : angle 1.42799 / 0.81 ( 4) hydrogen bonds : bond 0.04637 / 3.08 ( 387) hydrogen bonds : angle 4.32055 / 3.00 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.329 Fit side-chains REVERT: A 126 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 130 ASN cc_start: 0.8021 (m-40) cc_final: 0.7723 (m110) REVERT: B 219 ARG cc_start: 0.7249 (mtp180) cc_final: 0.7043 (ttm-80) REVERT: C 21 MET cc_start: 0.7166 (mtp) cc_final: 0.6801 (ttt) REVERT: S 223 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.5813 (t80) outliers start: 21 outliers final: 9 residues processed: 145 average time/residue: 0.1263 time to fit residues: 23.6065 Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 96 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.9174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 230 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 = 0.4221 r_free = 0.4221 target = 0.198429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170483 restraints weight = 9234.077| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.49 r_work: 0.3580 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9044 Z= 0.103 Angle : 0.482 5.712 12260 Z= 0.255 Chirality : 0.042 0.299 1406 Planarity : 0.004 0.061 1547 Dihedral : 5.269 59.375 1262 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.69 % Allowed : 25.16 % Favored : 73.15 % 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: 0.42 (0.25), residues: 1127 helix: 1.70 (0.27), residues: 380 sheet: 0.07 (0.31), residues: 283 loop : -0.75 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 114 TYR 0.020 0.001 TYR S 223 PHE 0.011 0.001 PHE B 199 TRP 0.008 0.001 TRP R 121 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9042) covalent geometry : angle 0.48087 / 0.25 (12256) SS BOND : bond 0.00093 / 0.04 ( 2) SS BOND : angle 1.55806 / 0.88 ( 4) hydrogen bonds : bond 0.04560 / 3.04 ( 387) hydrogen bonds : angle 4.18639 / 2.90 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.325 Fit side-chains REVERT: A 126 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 130 ASN cc_start: 0.8052 (m-40) cc_final: 0.7764 (m110) REVERT: B 43 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7923 (mp) REVERT: C 21 MET cc_start: 0.7384 (mtp) cc_final: 0.6998 (ttt) REVERT: S 223 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5955 (t80) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.1204 time to fit residues: 22.0917 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 230 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 = 0.4203 r_free = 0.4203 target = 0.196531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166805 restraints weight = 9171.493| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.51 r_work: 0.3544 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9044 Z= 0.125 Angle : 0.513 6.368 12260 Z= 0.270 Chirality : 0.042 0.284 1406 Planarity : 0.004 0.062 1547 Dihedral : 5.306 59.536 1262 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.96 % Allowed : 24.31 % Favored : 72.73 % 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: 0.42 (0.25), residues: 1127 helix: 1.69 (0.27), residues: 382 sheet: 0.07 (0.31), residues: 283 loop : -0.73 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 114 TYR 0.021 0.001 TYR S 223 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9042) covalent geometry : angle 0.51211 / 0.27 (12256) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 1.59114 / 0.90 ( 4) hydrogen bonds : bond 0.04984 / 3.33 ( 387) hydrogen bonds : angle 4.21318 / 2.93 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.381 Fit side-chains REVERT: A 126 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 130 ASN cc_start: 0.8044 (m-40) cc_final: 0.7711 (m110) REVERT: B 43 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 21 MET cc_start: 0.7311 (mtp) cc_final: 0.6935 (ttt) REVERT: S 223 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.5986 (t80) outliers start: 28 outliers final: 18 residues processed: 142 average time/residue: 0.1141 time to fit residues: 21.3258 Evaluate side-chains 136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 303 ASN A 89 GLN ** A 230 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 = 0.4216 r_free = 0.4216 target = 0.197979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166430 restraints weight = 9197.414| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.68 r_work: 0.3521 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9044 Z= 0.109 Angle : 0.489 6.052 12260 Z= 0.258 Chirality : 0.042 0.282 1406 Planarity : 0.004 0.061 1547 Dihedral : 5.224 59.457 1262 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.54 % Allowed : 24.42 % Favored : 73.04 % 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: 0.55 (0.25), residues: 1127 helix: 1.83 (0.27), residues: 382 sheet: 0.12 (0.31), residues: 283 loop : -0.68 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 114 TYR 0.020 0.001 TYR S 223 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9042) covalent geometry : angle 0.48828 / 0.26 (12256) SS BOND : bond 0.00149 / 0.08 ( 2) SS BOND : angle 1.45843 / 0.83 ( 4) hydrogen bonds : bond 0.04581 / 3.06 ( 387) hydrogen bonds : angle 4.08763 / 2.84 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.323 Fit side-chains REVERT: A 126 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 130 ASN cc_start: 0.8024 (m-40) cc_final: 0.7726 (m-40) REVERT: B 43 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7950 (mp) REVERT: C 21 MET cc_start: 0.7440 (mtp) cc_final: 0.7083 (ttt) REVERT: S 223 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5805 (t80) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.1102 time to fit residues: 20.6807 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 0.0060 chunk 86 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 230 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 = 0.4164 r_free = 0.4164 target = 0.192181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157651 restraints weight = 9123.629| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.85 r_work: 0.3424 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9044 Z= 0.208 Angle : 0.611 8.456 12260 Z= 0.318 Chirality : 0.046 0.290 1406 Planarity : 0.005 0.063 1547 Dihedral : 5.562 58.590 1262 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.49 % Allowed : 23.68 % Favored : 72.83 % 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: 0.15 (0.25), residues: 1127 helix: 1.42 (0.27), residues: 384 sheet: -0.09 (0.31), residues: 279 loop : -0.84 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 114 TYR 0.029 0.002 TYR S 223 PHE 0.016 0.002 PHE B 151 TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 9042) covalent geometry : angle 0.61036 / 0.32 (12256) SS BOND : bond 0.00189 / 0.10 ( 2) SS BOND : angle 2.08292 / 1.18 ( 4) hydrogen bonds : bond 0.06156 / 4.12 ( 387) hydrogen bonds : angle 4.46075 / 3.11 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: R 221 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8360 (ptp) REVERT: A 126 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: A 130 ASN cc_start: 0.8135 (m-40) cc_final: 0.7804 (m110) REVERT: B 43 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7948 (mp) REVERT: S 223 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6260 (t80) outliers start: 33 outliers final: 24 residues processed: 151 average time/residue: 0.1138 time to fit residues: 22.3579 Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 230 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 = 0.4181 r_free = 0.4181 target = 0.194111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160465 restraints weight = 9057.592| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.71 r_work: 0.3475 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9044 Z= 0.143 Angle : 0.542 6.873 12260 Z= 0.286 Chirality : 0.043 0.298 1406 Planarity : 0.004 0.058 1547 Dihedral : 5.483 59.650 1262 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.17 % Allowed : 24.21 % Favored : 72.62 % 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: 0.25 (0.25), residues: 1127 helix: 1.53 (0.27), residues: 384 sheet: -0.06 (0.31), residues: 283 loop : -0.81 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 114 TYR 0.025 0.001 TYR S 223 PHE 0.014 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9042) covalent geometry : angle 0.54131 / 0.29 (12256) SS BOND : bond 0.00110 / 0.05 ( 2) SS BOND : angle 1.74654 / 0.99 ( 4) hydrogen bonds : bond 0.05332 / 3.56 ( 387) hydrogen bonds : angle 4.30975 / 3.00 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 130 ASN cc_start: 0.8057 (m-40) cc_final: 0.7745 (m110) REVERT: B 43 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 198 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8485 (mt) REVERT: S 223 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5858 (t80) outliers start: 30 outliers final: 27 residues processed: 148 average time/residue: 0.1078 time to fit residues: 21.2415 Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.0040 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 89 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 230 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 = 0.4214 r_free = 0.4214 target = 0.197685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165792 restraints weight = 9163.425| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.69 r_work: 0.3527 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9044 Z= 0.106 Angle : 0.492 5.660 12260 Z= 0.262 Chirality : 0.042 0.280 1406 Planarity : 0.004 0.061 1547 Dihedral : 5.277 58.562 1262 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.96 % Allowed : 24.74 % Favored : 72.30 % 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: 0.49 (0.25), residues: 1127 helix: 1.82 (0.27), residues: 380 sheet: 0.09 (0.31), residues: 283 loop : -0.75 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 114 TYR 0.020 0.001 TYR S 223 PHE 0.011 0.001 PHE B 199 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9042) covalent geometry : angle 0.49183 / 0.26 (12256) SS BOND : bond 0.00189 / 0.10 ( 2) SS BOND : angle 1.39674 / 0.79 ( 4) hydrogen bonds : bond 0.04452 / 2.96 ( 387) hydrogen bonds : angle 4.05878 / 2.81 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.325 Fit side-chains REVERT: A 28 THR cc_start: 0.8008 (m) cc_final: 0.7767 (p) REVERT: A 126 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 130 ASN cc_start: 0.8007 (m-40) cc_final: 0.7726 (m-40) REVERT: B 43 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7882 (mp) REVERT: S 223 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5420 (t80) outliers start: 28 outliers final: 22 residues processed: 144 average time/residue: 0.1094 time to fit residues: 20.9293 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 101 optimal weight: 0.0670 chunk 84 optimal weight: 20.0000 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 230 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 = 0.4196 r_free = 0.4196 target = 0.195678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161280 restraints weight = 9034.891| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.71 r_work: 0.3528 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9044 Z= 0.106 Angle : 0.499 6.017 12260 Z= 0.263 Chirality : 0.042 0.284 1406 Planarity : 0.004 0.060 1547 Dihedral : 5.227 58.547 1262 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.64 % Allowed : 25.16 % Favored : 72.20 % 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: 0.58 (0.25), residues: 1127 helix: 1.89 (0.27), residues: 381 sheet: 0.17 (0.31), residues: 283 loop : -0.71 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 114 TYR 0.020 0.001 TYR S 223 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9042) covalent geometry : angle 0.49823 / 0.26 (12256) SS BOND : bond 0.00163 / 0.08 ( 2) SS BOND : angle 1.44275 / 0.82 ( 4) hydrogen bonds : bond 0.04425 / 2.95 ( 387) hydrogen bonds : angle 4.01336 / 2.78 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.10 seconds wall clock time: 38 minutes 18.55 seconds (2298.55 seconds total)