Starting phenix.real_space_refine on Thu Jul 2 05:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0m_65508/07_2026/9w0m_65508.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4382 2.51 5 N 1172 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6881 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2133 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "D" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1746 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 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 Time building chain proxies: 1.29, per 1000 atoms: 0.19 Number of scatterers: 6881 At special positions: 0 Unit cell: (77.33, 99.275, 129.58, 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 50 16.00 O 1277 8.00 N 1172 7.00 C 4382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 264 " 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: 0.44 Conformation dependent library (CDL) restraints added in 340.9 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 45.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.766A pdb=" N VAL A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 56 removed outlier: 3.734A pdb=" N GLN A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 48 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 70 through 94 removed outlier: 3.746A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 136 removed outlier: 3.512A pdb=" N ALA A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 170 removed outlier: 4.013A pdb=" N MET A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.939A pdb=" N GLY A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 216 removed outlier: 3.975A pdb=" N VAL A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 226 through 259 removed outlier: 3.506A pdb=" N ALA A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Proline residue: A 248 - end of helix removed outlier: 4.447A pdb=" N ILE A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.881A pdb=" N PHE A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 294 removed outlier: 3.855A pdb=" N LEU A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.517A pdb=" N TRP A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 4.281A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.850A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 4.262A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.575A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.412A pdb=" N SER B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.513A pdb=" N LYS D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN D 22 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 removed outlier: 3.799A pdb=" N CYS D 47 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 removed outlier: 3.900A pdb=" N MET D 53 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.163A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 256 removed outlier: 3.920A pdb=" N MET D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 274 through 279 removed outlier: 4.302A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.910A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 removed outlier: 4.224A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 306 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 352 removed outlier: 3.845A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.602A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP B 82 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.656A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.524A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.158A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.133A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.826A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 320 removed outlier: 7.015A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 191 removed outlier: 3.554A pdb=" N VAL D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 198 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 189 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA D 220 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 35 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE D 222 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU D 37 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS D 224 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 322 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 268 " --> pdb=" O HIS D 322 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 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: 0.79 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 1622 1.46 - 1.58: 3092 1.58 - 1.70: 0 1.70 - 1.81: 67 Bond restraints: 7011 Sorted by residual: bond pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.73e-01 bond pdb=" CG LYS B 78 " pdb=" CD LYS B 78 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.99e-01 bond pdb=" N GLY D 42 " pdb=" CA GLY D 42 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.13e-01 bond pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 1.462 1.473 -0.011 1.54e-02 4.22e+03 5.18e-01 bond pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.54e-02 4.22e+03 4.84e-01 ... (remaining 7006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 9381 1.69 - 3.39: 100 3.39 - 5.08: 22 5.08 - 6.78: 6 6.78 - 8.47: 2 Bond angle restraints: 9511 Sorted by residual: angle pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " pdb=" CD LYS B 78 " ideal model delta sigma weight residual 111.30 119.07 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 113.42 110.35 3.07 1.17e+00 7.31e-01 6.88e+00 angle pdb=" C GLN C 58 " pdb=" N ASN C 59 " pdb=" CA ASN C 59 " ideal model delta sigma weight residual 121.80 127.90 -6.10 2.44e+00 1.68e-01 6.25e+00 angle pdb=" CA LEU D 283 " pdb=" CB LEU D 283 " pdb=" CG LEU D 283 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.86e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.08 125.07 -2.99 1.47e+00 4.63e-01 4.15e+00 ... (remaining 9506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3729 16.26 - 32.51: 346 32.51 - 48.76: 88 48.76 - 65.02: 11 65.02 - 81.27: 5 Dihedral angle restraints: 4179 sinusoidal: 1585 harmonic: 2594 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual 93.00 124.61 -31.61 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA TRP A 290 " pdb=" C TRP A 290 " pdb=" N ARG A 291 " pdb=" CA ARG A 291 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA MET D 18 " pdb=" C MET D 18 " pdb=" N ILE D 19 " pdb=" CA ILE D 19 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 4176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 639 0.026 - 0.053: 302 0.053 - 0.079: 120 0.079 - 0.105: 33 0.105 - 0.131: 24 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA LEU A 247 " pdb=" N LEU A 247 " pdb=" C LEU A 247 " pdb=" CB LEU A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1115 not shown) Planarity restraints: 1194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 290 " -0.010 2.00e-02 2.50e+03 9.71e-03 2.36e+00 pdb=" CG TRP A 290 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 290 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 290 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 290 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 290 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 290 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 290 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 290 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 290 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 93 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 94 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO B 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 1191 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1395 2.78 - 3.31: 6844 3.31 - 3.84: 11172 3.84 - 4.37: 13057 4.37 - 4.90: 21947 Nonbonded interactions: 54415 Sorted by model distance: nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.247 3.120 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OE1 GLU A 129 " model vdw 2.279 3.040 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.285 3.120 nonbonded pdb=" OH TYR D 290 " pdb=" OE2 GLU D 298 " model vdw 2.289 3.040 ... (remaining 54410 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 group one per residue 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: 1.280 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.002 0.030 7013 Z= 0.080 Angle : 0.482 8.470 9515 Z= 0.233 Chirality : 0.038 0.131 1118 Planarity : 0.002 0.037 1194 Dihedral : 13.583 81.274 2487 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 (0.29), residues: 872 helix: 0.23 (0.30), residues: 310 sheet: 0.72 (0.51), residues: 125 loop : -0.44 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 21 TYR 0.013 0.001 TYR A 69 PHE 0.014 0.001 PHE B 241 TRP 0.026 0.001 TRP A 290 HIS 0.006 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.08 ( 7011) covalent geometry : angle 0.48192 / 0.23 ( 9511) SS BOND : bond 0.00206 / 0.11 ( 2) SS BOND : angle 0.30678 / 0.18 ( 4) hydrogen bonds : bond 0.28644 / 18.94 ( 278) hydrogen bonds : angle 8.05936 / 5.73 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7011 (ppp) cc_final: 0.6795 (ttp) REVERT: D 24 ARG cc_start: 0.5935 (ttt180) cc_final: 0.5703 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0689 time to fit residues: 15.5536 Evaluate side-chains 133 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125068 restraints weight = 11762.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125419 restraints weight = 8567.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127397 restraints weight = 6907.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127805 restraints weight = 5255.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.128008 restraints weight = 5060.520| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7013 Z= 0.150 Angle : 0.598 9.482 9515 Z= 0.305 Chirality : 0.042 0.180 1118 Planarity : 0.003 0.032 1194 Dihedral : 3.933 34.751 949 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.61 % Allowed : 12.21 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 872 helix: 0.59 (0.30), residues: 311 sheet: 0.66 (0.48), residues: 141 loop : -0.33 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.020 0.001 TYR A 272 PHE 0.018 0.001 PHE B 199 TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 7011) covalent geometry : angle 0.59833 / 0.30 ( 9511) SS BOND : bond 0.00130 / 0.07 ( 2) SS BOND : angle 0.70613 / 0.40 ( 4) hydrogen bonds : bond 0.04521 / 2.94 ( 278) hydrogen bonds : angle 5.26918 / 3.77 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7719 (t80) cc_final: 0.7412 (t80) REVERT: C 38 MET cc_start: 0.7031 (mtm) cc_final: 0.6614 (mtm) REVERT: B 90 VAL cc_start: 0.6414 (p) cc_final: 0.6214 (p) REVERT: D 18 MET cc_start: 0.7924 (ppp) cc_final: 0.7720 (ppp) outliers start: 12 outliers final: 6 residues processed: 164 average time/residue: 0.0689 time to fit residues: 15.2109 Evaluate side-chains 149 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 298 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 266 HIS D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.153661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123978 restraints weight = 11695.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123802 restraints weight = 9264.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.125232 restraints weight = 7150.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.125667 restraints weight = 6026.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125999 restraints weight = 5623.442| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7013 Z= 0.114 Angle : 0.544 9.179 9515 Z= 0.277 Chirality : 0.041 0.176 1118 Planarity : 0.003 0.026 1194 Dihedral : 3.703 21.154 949 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.15 % Allowed : 16.24 % Favored : 81.61 % 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: 0.23 (0.29), residues: 872 helix: 0.69 (0.30), residues: 327 sheet: 0.52 (0.47), residues: 141 loop : -0.32 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.019 0.001 TYR A 272 PHE 0.024 0.001 PHE B 241 TRP 0.022 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7011) covalent geometry : angle 0.54424 / 0.28 ( 9511) SS BOND : bond 0.00156 / 0.08 ( 2) SS BOND : angle 0.55240 / 0.32 ( 4) hydrogen bonds : bond 0.03885 / 2.52 ( 278) hydrogen bonds : angle 4.91817 / 3.53 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.185 Fit side-chains REVERT: A 75 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7355 (tt) REVERT: A 198 PHE cc_start: 0.7677 (t80) cc_final: 0.7410 (t80) REVERT: A 231 LEU cc_start: 0.7135 (tp) cc_final: 0.6915 (tp) REVERT: B 262 MET cc_start: 0.5883 (tpp) cc_final: 0.5668 (mmt) REVERT: D 18 MET cc_start: 0.7971 (ppp) cc_final: 0.7662 (ppp) outliers start: 16 outliers final: 9 residues processed: 156 average time/residue: 0.0685 time to fit residues: 14.4030 Evaluate side-chains 146 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 298 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN ** B 17 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 = 0.4187 r_free = 0.4187 target = 0.151211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118824 restraints weight = 11739.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121717 restraints weight = 7882.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123797 restraints weight = 5969.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.125227 restraints weight = 4893.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.125734 restraints weight = 4241.235| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7013 Z= 0.120 Angle : 0.555 8.862 9515 Z= 0.280 Chirality : 0.041 0.165 1118 Planarity : 0.003 0.030 1194 Dihedral : 3.779 19.797 949 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.82 % Allowed : 18.79 % Favored : 78.39 % 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: 0.21 (0.30), residues: 872 helix: 0.69 (0.30), residues: 326 sheet: 0.39 (0.47), residues: 146 loop : -0.31 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.012 0.001 TYR A 272 PHE 0.026 0.001 PHE B 241 TRP 0.025 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7011) covalent geometry : angle 0.55501 / 0.28 ( 9511) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 0.61861 / 0.35 ( 4) hydrogen bonds : bond 0.03383 / 2.19 ( 278) hydrogen bonds : angle 4.72252 / 3.38 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7349 (tt) REVERT: A 198 PHE cc_start: 0.7685 (t80) cc_final: 0.7149 (t80) REVERT: A 290 TRP cc_start: 0.6428 (t60) cc_final: 0.5889 (t60) REVERT: D 18 MET cc_start: 0.7850 (ppp) cc_final: 0.7533 (ppp) REVERT: D 21 ARG cc_start: 0.7261 (ptp90) cc_final: 0.6946 (ptm160) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 0.0728 time to fit residues: 15.1955 Evaluate side-chains 151 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 298 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115257 restraints weight = 11840.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115354 restraints weight = 8782.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116252 restraints weight = 7300.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116586 restraints weight = 6301.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.117991 restraints weight = 5769.483| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7013 Z= 0.162 Angle : 0.604 9.010 9515 Z= 0.306 Chirality : 0.043 0.255 1118 Planarity : 0.003 0.029 1194 Dihedral : 4.079 15.934 949 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.68 % Allowed : 20.67 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 872 helix: 0.60 (0.31), residues: 327 sheet: -0.06 (0.46), residues: 145 loop : -0.29 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.024 0.002 TYR A 69 PHE 0.023 0.002 PHE B 241 TRP 0.037 0.003 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7011) covalent geometry : angle 0.60370 / 0.31 ( 9511) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 0.86549 / 0.48 ( 4) hydrogen bonds : bond 0.03342 / 2.16 ( 278) hydrogen bonds : angle 4.77814 / 3.45 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.173 Fit side-chains REVERT: A 75 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7440 (tt) REVERT: A 149 LEU cc_start: 0.5922 (mt) cc_final: 0.5539 (mt) REVERT: A 198 PHE cc_start: 0.7712 (t80) cc_final: 0.7476 (t80) REVERT: A 290 TRP cc_start: 0.6202 (t60) cc_final: 0.5854 (t60) REVERT: B 6 GLU cc_start: 0.6640 (mp0) cc_final: 0.6315 (mp0) REVERT: B 65 THR cc_start: 0.6233 (p) cc_final: 0.5999 (p) REVERT: D 21 ARG cc_start: 0.7345 (ptp90) cc_final: 0.7144 (ptp90) outliers start: 20 outliers final: 12 residues processed: 160 average time/residue: 0.0715 time to fit residues: 15.3090 Evaluate side-chains 150 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 298 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114279 restraints weight = 11858.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113977 restraints weight = 8524.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115887 restraints weight = 7102.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117054 restraints weight = 5281.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117292 restraints weight = 4833.263| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7013 Z= 0.150 Angle : 0.608 9.040 9515 Z= 0.307 Chirality : 0.043 0.211 1118 Planarity : 0.003 0.026 1194 Dihedral : 4.124 17.405 949 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.55 % Allowed : 22.28 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 872 helix: 0.59 (0.31), residues: 324 sheet: 0.00 (0.47), residues: 136 loop : -0.50 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.010 0.001 TYR A 272 PHE 0.022 0.001 PHE B 241 TRP 0.033 0.003 TRP B 339 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7011) covalent geometry : angle 0.60837 / 0.31 ( 9511) SS BOND : bond 0.00094 / 0.05 ( 2) SS BOND : angle 0.84125 / 0.47 ( 4) hydrogen bonds : bond 0.03192 / 2.08 ( 278) hydrogen bonds : angle 4.77014 / 3.46 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.267 Fit side-chains REVERT: A 75 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7434 (tt) REVERT: A 254 LEU cc_start: 0.8405 (mt) cc_final: 0.7564 (tt) REVERT: A 290 TRP cc_start: 0.6028 (t60) cc_final: 0.5747 (t60) REVERT: B 6 GLU cc_start: 0.6802 (mp0) cc_final: 0.6468 (mp0) REVERT: B 65 THR cc_start: 0.6395 (p) cc_final: 0.6166 (p) REVERT: B 172 GLU cc_start: 0.7563 (pm20) cc_final: 0.7327 (pm20) REVERT: D 21 ARG cc_start: 0.7426 (ptp90) cc_final: 0.7220 (ptp90) outliers start: 19 outliers final: 11 residues processed: 160 average time/residue: 0.0649 time to fit residues: 14.2030 Evaluate side-chains 153 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 298 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 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 = 0.4085 r_free = 0.4085 target = 0.143685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113122 restraints weight = 11714.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113044 restraints weight = 9900.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114156 restraints weight = 8134.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114643 restraints weight = 7062.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.115052 restraints weight = 6252.096| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7013 Z= 0.183 Angle : 0.656 9.646 9515 Z= 0.330 Chirality : 0.044 0.191 1118 Planarity : 0.003 0.027 1194 Dihedral : 4.385 17.765 949 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.95 % Allowed : 23.22 % Favored : 73.83 % 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: -0.27 (0.29), residues: 872 helix: 0.44 (0.30), residues: 325 sheet: -0.38 (0.44), residues: 152 loop : -0.49 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 304 TYR 0.026 0.002 TYR A 69 PHE 0.020 0.002 PHE B 241 TRP 0.040 0.003 TRP B 339 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 7011) covalent geometry : angle 0.65556 / 0.33 ( 9511) SS BOND : bond 0.00105 / 0.05 ( 2) SS BOND : angle 1.01256 / 0.57 ( 4) hydrogen bonds : bond 0.03320 / 2.16 ( 278) hydrogen bonds : angle 4.93165 / 3.58 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.180 Fit side-chains REVERT: A 75 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 89 ASN cc_start: 0.7824 (t0) cc_final: 0.7197 (t0) REVERT: B 65 THR cc_start: 0.6289 (p) cc_final: 0.6057 (p) REVERT: B 118 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (t0) REVERT: B 246 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8358 (m-30) outliers start: 22 outliers final: 14 residues processed: 163 average time/residue: 0.0654 time to fit residues: 14.3112 Evaluate side-chains 157 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 195 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116899 restraints weight = 11568.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117370 restraints weight = 8717.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118139 restraints weight = 6857.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118342 restraints weight = 6113.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.118862 restraints weight = 5844.511| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7013 Z= 0.141 Angle : 0.637 8.972 9515 Z= 0.321 Chirality : 0.043 0.178 1118 Planarity : 0.003 0.027 1194 Dihedral : 4.226 20.460 949 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.68 % Allowed : 24.70 % 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: -0.22 (0.29), residues: 872 helix: 0.44 (0.30), residues: 327 sheet: -0.25 (0.46), residues: 143 loop : -0.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 68 TYR 0.020 0.001 TYR A 272 PHE 0.025 0.001 PHE D 199 TRP 0.032 0.003 TRP B 339 HIS 0.006 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7011) covalent geometry : angle 0.63728 / 0.32 ( 9511) SS BOND : bond 0.00085 / 0.04 ( 2) SS BOND : angle 0.78088 / 0.44 ( 4) hydrogen bonds : bond 0.03068 / 2.00 ( 278) hydrogen bonds : angle 4.77773 / 3.48 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.390 Fit side-chains REVERT: A 75 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 89 ASN cc_start: 0.7810 (t0) cc_final: 0.7176 (t0) REVERT: B 6 GLU cc_start: 0.6848 (mp0) cc_final: 0.6583 (mp0) REVERT: B 65 THR cc_start: 0.6134 (p) cc_final: 0.5898 (p) REVERT: B 99 TRP cc_start: 0.7787 (m100) cc_final: 0.7455 (m100) REVERT: B 246 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: D 247 MET cc_start: 0.7149 (ptp) cc_final: 0.6675 (ptt) REVERT: D 268 LEU cc_start: 0.6117 (mm) cc_final: 0.5830 (mm) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 0.0594 time to fit residues: 12.1966 Evaluate side-chains 156 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 322 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117255 restraints weight = 11544.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117131 restraints weight = 8559.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117872 restraints weight = 7086.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.118136 restraints weight = 6321.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119656 restraints weight = 5903.499| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7013 Z= 0.145 Angle : 0.655 8.922 9515 Z= 0.328 Chirality : 0.043 0.188 1118 Planarity : 0.003 0.027 1194 Dihedral : 4.255 20.015 949 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.28 % Allowed : 25.37 % Favored : 72.35 % 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: -0.33 (0.29), residues: 872 helix: 0.36 (0.30), residues: 332 sheet: -0.25 (0.47), residues: 143 loop : -0.59 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.018 0.001 TYR A 272 PHE 0.037 0.002 PHE B 241 TRP 0.034 0.003 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7011) covalent geometry : angle 0.65528 / 0.33 ( 9511) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.75881 / 0.43 ( 4) hydrogen bonds : bond 0.03075 / 2.01 ( 278) hydrogen bonds : angle 4.78856 / 3.47 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.261 Fit side-chains REVERT: A 69 TYR cc_start: 0.5810 (t80) cc_final: 0.5559 (t80) REVERT: A 75 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7430 (tt) REVERT: A 89 ASN cc_start: 0.7760 (t0) cc_final: 0.7118 (t0) REVERT: A 290 TRP cc_start: 0.6200 (t60) cc_final: 0.5994 (t60) REVERT: A 291 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6990 (mmm160) REVERT: B 6 GLU cc_start: 0.6848 (mp0) cc_final: 0.6572 (mp0) REVERT: B 65 THR cc_start: 0.6184 (p) cc_final: 0.5966 (p) REVERT: B 246 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: B 264 TYR cc_start: 0.7903 (m-10) cc_final: 0.7246 (m-10) REVERT: D 247 MET cc_start: 0.7209 (ptp) cc_final: 0.6790 (ptt) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.0590 time to fit residues: 12.1551 Evaluate side-chains 151 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 195 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN ** B 17 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 = 0.4174 r_free = 0.4174 target = 0.150722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119789 restraints weight = 11529.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.120426 restraints weight = 8112.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120841 restraints weight = 6648.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.121016 restraints weight = 6206.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123001 restraints weight = 5714.910| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7013 Z= 0.121 Angle : 0.639 9.229 9515 Z= 0.318 Chirality : 0.043 0.196 1118 Planarity : 0.003 0.027 1194 Dihedral : 4.124 19.301 949 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.88 % Allowed : 25.64 % Favored : 72.48 % 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: -0.28 (0.29), residues: 872 helix: 0.46 (0.30), residues: 332 sheet: -0.36 (0.47), residues: 144 loop : -0.56 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.017 0.001 TYR A 272 PHE 0.035 0.002 PHE B 241 TRP 0.029 0.003 TRP B 339 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7011) covalent geometry : angle 0.63948 / 0.32 ( 9511) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.56878 / 0.32 ( 4) hydrogen bonds : bond 0.02898 / 1.90 ( 278) hydrogen bonds : angle 4.66056 / 3.37 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.241 Fit side-chains REVERT: A 89 ASN cc_start: 0.7714 (t0) cc_final: 0.7024 (t0) REVERT: A 168 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4921 (mm) REVERT: A 290 TRP cc_start: 0.6285 (t60) cc_final: 0.6082 (t60) REVERT: A 291 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6978 (mmm160) REVERT: B 6 GLU cc_start: 0.6908 (mp0) cc_final: 0.6673 (mp0) REVERT: B 65 THR cc_start: 0.6203 (p) cc_final: 0.5987 (p) REVERT: B 246 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: D 199 PHE cc_start: 0.8748 (m-10) cc_final: 0.8455 (m-10) REVERT: D 247 MET cc_start: 0.7167 (ptp) cc_final: 0.6746 (ptt) outliers start: 14 outliers final: 9 residues processed: 155 average time/residue: 0.0656 time to fit residues: 13.9946 Evaluate side-chains 148 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain D residue 195 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS D 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.150219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120784 restraints weight = 11499.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.120793 restraints weight = 8533.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121660 restraints weight = 6985.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122174 restraints weight = 5987.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122295 restraints weight = 5550.792| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7013 Z= 0.126 Angle : 0.649 9.761 9515 Z= 0.320 Chirality : 0.043 0.283 1118 Planarity : 0.003 0.027 1194 Dihedral : 4.120 20.120 949 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.88 % Allowed : 26.04 % Favored : 72.08 % 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: -0.34 (0.29), residues: 872 helix: 0.46 (0.30), residues: 327 sheet: -0.35 (0.46), residues: 144 loop : -0.65 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.025 0.001 TYR A 69 PHE 0.035 0.002 PHE B 241 TRP 0.048 0.003 TRP B 339 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7011) covalent geometry : angle 0.64944 / 0.32 ( 9511) SS BOND : bond 0.00127 / 0.07 ( 2) SS BOND : angle 0.59911 / 0.34 ( 4) hydrogen bonds : bond 0.02930 / 1.91 ( 278) hydrogen bonds : angle 4.74615 / 3.43 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1040.03 seconds wall clock time: 18 minutes 47.56 seconds (1127.56 seconds total)