Starting phenix.real_space_refine on Wed Jun 3 19:02:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.map" model { file = "/net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kag_62208/06_2026/9kag_62208.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.060 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 28 5.16 5 C 5200 2.51 5 N 1378 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8216 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1605 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 198} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2506 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 319} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1599 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 198} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2506 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 319} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.08, per 1000 atoms: 0.25 Number of scatterers: 8216 At special positions: 0 Unit cell: (132.75, 96.75, 110.25, 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 28 16.00 O 1610 8.00 N 1378 7.00 C 5200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.69 Conformation dependent library (CDL) restraints added in 308.2 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 68.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 removed outlier: 3.769A pdb=" N GLU A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.787A pdb=" N LEU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.583A pdb=" N ILE A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.657A pdb=" N LEU A 239 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 241 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.614A pdb=" N LEU B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.548A pdb=" N SER B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.765A pdb=" N GLU B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 153 removed outlier: 3.664A pdb=" N VAL B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 184 removed outlier: 3.772A pdb=" N GLN B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 removed outlier: 3.634A pdb=" N LEU B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ARG B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 221 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 246 removed outlier: 3.764A pdb=" N ALA B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.502A pdb=" N TYR B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 282 removed outlier: 3.917A pdb=" N ILE B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 313 removed outlier: 3.527A pdb=" N CYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.573A pdb=" N PHE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.901A pdb=" N ARG B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.547A pdb=" N LEU B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 396 through 412 removed outlier: 4.162A pdb=" N VAL B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 96 removed outlier: 3.585A pdb=" N ALA C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.926A pdb=" N GLU C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 132 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.514A pdb=" N LEU C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.856A pdb=" N ILE C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.905A pdb=" N LEU C 239 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 241 " --> pdb=" O MET C 237 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.638A pdb=" N LEU D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 removed outlier: 3.561A pdb=" N LEU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.983A pdb=" N GLU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 153 removed outlier: 3.528A pdb=" N ALA D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 141 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 184 removed outlier: 3.912A pdb=" N GLN D 162 " --> pdb=" O THR D 158 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 199 through 221 removed outlier: 3.554A pdb=" N LEU D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 245 removed outlier: 3.738A pdb=" N ALA D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.906A pdb=" N ILE D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 313 removed outlier: 3.540A pdb=" N CYS D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.616A pdb=" N ALA D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.739A pdb=" N ARG D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 348 " --> pdb=" O GLN D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 370 through 390 removed outlier: 3.509A pdb=" N LEU D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.504A pdb=" N SER D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 410 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 147 removed outlier: 3.948A pdb=" N TRP A 142 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 172 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE A 170 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N TYR A 146 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 14.159A pdb=" N GLY A 168 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A 167 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 188 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 169 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 186 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER A 204 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU A 217 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 206 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE A 215 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 246 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 259 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 253 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A 271 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU A 144 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'C' and resid 141 through 147 removed outlier: 4.004A pdb=" N TRP C 142 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 144 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE C 170 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N TYR C 146 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 14.162A pdb=" N GLY C 168 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 169 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER C 204 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 217 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 206 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE C 215 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 246 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 259 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL C 253 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 267 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER C 147 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 269 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 145 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS C 141 " --> pdb=" O ALA C 273 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1443 1.32 - 1.44: 1986 1.44 - 1.57: 4853 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8330 Sorted by residual: bond pdb=" N LYS D 134 " pdb=" CA LYS D 134 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.95e+01 bond pdb=" C PRO B 343 " pdb=" O PRO B 343 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" N ILE D 128 " pdb=" CA ILE D 128 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" N VAL C 138 " pdb=" CA VAL C 138 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL B 406 " pdb=" CA VAL B 406 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.28e+00 ... (remaining 8325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10477 1.73 - 3.45: 677 3.45 - 5.18: 89 5.18 - 6.90: 17 6.90 - 8.63: 2 Bond angle restraints: 11262 Sorted by residual: angle pdb=" O LYS D 134 " pdb=" C LYS D 134 " pdb=" N ARG D 135 " ideal model delta sigma weight residual 121.47 125.11 -3.64 7.50e-01 1.78e+00 2.35e+01 angle pdb=" N VAL A 145 " pdb=" CA VAL A 145 " pdb=" C VAL A 145 " ideal model delta sigma weight residual 113.71 109.19 4.52 9.50e-01 1.11e+00 2.26e+01 angle pdb=" N VAL C 145 " pdb=" CA VAL C 145 " pdb=" C VAL C 145 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.18e+01 angle pdb=" C LYS D 134 " pdb=" CA LYS D 134 " pdb=" CB LYS D 134 " ideal model delta sigma weight residual 117.07 110.93 6.14 1.44e+00 4.82e-01 1.82e+01 angle pdb=" C PRO B 343 " pdb=" CA PRO B 343 " pdb=" CB PRO B 343 " ideal model delta sigma weight residual 112.55 106.51 6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 11257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4386 17.06 - 34.13: 504 34.13 - 51.19: 141 51.19 - 68.26: 45 68.26 - 85.32: 12 Dihedral angle restraints: 5088 sinusoidal: 2004 harmonic: 3084 Sorted by residual: dihedral pdb=" CA PHE C 242 " pdb=" C PHE C 242 " pdb=" N ASN C 243 " pdb=" CA ASN C 243 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE A 242 " pdb=" C PHE A 242 " pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA THR D 332 " pdb=" C THR D 332 " pdb=" N ALA D 333 " pdb=" CA ALA D 333 " ideal model delta harmonic sigma weight residual -180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1079 0.064 - 0.129: 211 0.129 - 0.193: 33 0.193 - 0.258: 6 0.258 - 0.322: 3 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL D 99 " pdb=" CA VAL D 99 " pdb=" CG1 VAL D 99 " pdb=" CG2 VAL D 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ARG D 201 " pdb=" N ARG D 201 " pdb=" C ARG D 201 " pdb=" CB ARG D 201 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1329 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.363 9.50e-02 1.11e+02 1.63e-01 1.63e+01 pdb=" NE ARG B 137 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 137 " 0.330 9.50e-02 1.11e+02 1.48e-01 1.35e+01 pdb=" NE ARG D 137 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 137 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 137 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 137 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 118 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO D 119 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.032 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1471 2.77 - 3.30: 8339 3.30 - 3.83: 12790 3.83 - 4.37: 14965 4.37 - 4.90: 25033 Nonbonded interactions: 62598 Sorted by model distance: nonbonded pdb=" OG1 THR C 107 " pdb=" OE1 GLU C 109 " model vdw 2.236 3.040 nonbonded pdb=" O TYR D 263 " pdb=" OG SER D 268 " model vdw 2.257 3.040 nonbonded pdb=" N GLU D 156 " pdb=" OE1 GLU D 156 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS A 154 " pdb=" OD1 ASP B 250 " model vdw 2.271 3.120 nonbonded pdb=" OE2 GLU B 169 " pdb=" OG1 THR B 173 " model vdw 2.290 3.040 ... (remaining 62593 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 189 or (resid 190 through 191 and (name N or na \ me CA or name C or name O or name CB )) or resid 192 through 270 or (resid 271 t \ hrough 273 and (name N or name CA or name C or name O or name CB )) or resid 274 \ through 278)) selection = (chain 'C' and (resid 74 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 278)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.480 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 8.870 Find NCS groups from input model: 0.110 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.006 0.042 8330 Z= 0.425 Angle : 0.864 8.628 11262 Z= 0.597 Chirality : 0.055 0.322 1332 Planarity : 0.007 0.163 1448 Dihedral : 16.805 85.320 3088 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.75 % Favored : 96.39 % Rotamer: Outliers : 1.35 % Allowed : 28.06 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.80 (0.26), residues: 1054 helix: 1.13 (0.20), residues: 588 sheet: -0.13 (0.45), residues: 140 loop : -0.06 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 374 TYR 0.018 0.002 TYR D 408 PHE 0.012 0.001 PHE C 170 TRP 0.005 0.001 TRP C 142 HIS 0.005 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.42 ( 8330) covalent geometry : angle 0.86370 / 0.60 (11262) hydrogen bonds : bond 0.27306 / 18.73 ( 504) hydrogen bonds : angle 7.05894 / 4.84 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 420 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 158 LYS cc_start: 0.8818 (mttt) cc_final: 0.8604 (mttt) REVERT: B 102 ASP cc_start: 0.7909 (m-30) cc_final: 0.7605 (m-30) REVERT: B 127 GLN cc_start: 0.7967 (mt0) cc_final: 0.7420 (mt0) REVERT: B 129 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5866 (p90) REVERT: B 163 ARG cc_start: 0.8852 (mmp80) cc_final: 0.8461 (mmp80) REVERT: B 166 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7381 (mt-10) REVERT: B 244 GLN cc_start: 0.8207 (tt0) cc_final: 0.7793 (tp40) REVERT: B 257 ASP cc_start: 0.7911 (m-30) cc_final: 0.7682 (m-30) REVERT: B 266 THR cc_start: 0.8899 (m) cc_final: 0.8641 (p) REVERT: B 306 ASP cc_start: 0.7728 (m-30) cc_final: 0.7429 (m-30) REVERT: B 347 GLU cc_start: 0.7957 (pm20) cc_final: 0.7722 (pm20) REVERT: B 403 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 407 LYS cc_start: 0.8687 (tttt) cc_final: 0.8483 (ttmm) REVERT: C 89 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8251 (mtmt) REVERT: C 93 TYR cc_start: 0.7645 (m-10) cc_final: 0.7445 (m-80) REVERT: C 110 LYS cc_start: 0.8989 (mttt) cc_final: 0.8700 (mttt) REVERT: C 119 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 120 LEU cc_start: 0.8824 (tp) cc_final: 0.8575 (tp) REVERT: D 102 ASP cc_start: 0.7871 (m-30) cc_final: 0.7581 (m-30) REVERT: D 201 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7629 (ttt180) REVERT: D 249 PHE cc_start: 0.8913 (m-80) cc_final: 0.8638 (m-80) REVERT: D 289 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 302 PHE cc_start: 0.8848 (m-80) cc_final: 0.8538 (m-80) REVERT: D 306 ASP cc_start: 0.7805 (m-30) cc_final: 0.7431 (m-30) REVERT: D 309 LEU cc_start: 0.8301 (tp) cc_final: 0.8012 (tp) REVERT: D 347 GLU cc_start: 0.7844 (mp0) cc_final: 0.7263 (mp0) outliers start: 12 outliers final: 5 residues processed: 424 average time/residue: 0.1076 time to fit residues: 59.4601 Evaluate side-chains 421 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 414 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 201 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 297 ASN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN D 195 HIS D 196 GLN D 220 ASN D 290 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102749 restraints weight = 16411.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106663 restraints weight = 7990.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109232 restraints weight = 4893.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110907 restraints weight = 3477.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112170 restraints weight = 2732.118| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8330 Z= 0.205 Angle : 0.606 7.078 11262 Z= 0.329 Chirality : 0.044 0.214 1332 Planarity : 0.004 0.057 1448 Dihedral : 5.332 55.005 1152 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.51 % Favored : 96.30 % Rotamer: Outliers : 4.60 % Allowed : 25.48 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.27), residues: 1054 helix: 2.21 (0.20), residues: 612 sheet: 0.04 (0.46), residues: 140 loop : -0.17 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 156 TYR 0.020 0.002 TYR B 408 PHE 0.022 0.002 PHE C 170 TRP 0.007 0.001 TRP D 216 HIS 0.004 0.001 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 8330) covalent geometry : angle 0.60588 / 0.33 (11262) hydrogen bonds : bond 0.06935 / 4.71 ( 504) hydrogen bonds : angle 4.67895 / 3.23 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 422 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 94 SER cc_start: 0.9002 (m) cc_final: 0.8773 (p) REVERT: B 99 VAL cc_start: 0.8472 (p) cc_final: 0.8271 (m) REVERT: B 102 ASP cc_start: 0.7994 (m-30) cc_final: 0.7713 (m-30) REVERT: B 103 LEU cc_start: 0.8437 (mm) cc_final: 0.8032 (mm) REVERT: B 109 ASN cc_start: 0.8633 (t0) cc_final: 0.8403 (t0) REVERT: B 129 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5889 (p90) REVERT: B 210 MET cc_start: 0.8235 (mtp) cc_final: 0.8018 (mtt) REVERT: B 244 GLN cc_start: 0.8433 (tt0) cc_final: 0.7938 (tp40) REVERT: B 257 ASP cc_start: 0.7919 (m-30) cc_final: 0.7638 (m-30) REVERT: B 261 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: B 306 ASP cc_start: 0.7635 (m-30) cc_final: 0.7190 (m-30) REVERT: B 328 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8504 (tttt) REVERT: B 347 GLU cc_start: 0.8052 (pm20) cc_final: 0.7683 (pm20) REVERT: B 403 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 410 LEU cc_start: 0.8883 (mp) cc_final: 0.8663 (mm) REVERT: C 89 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8365 (mtmt) REVERT: C 93 TYR cc_start: 0.7877 (m-10) cc_final: 0.7598 (m-80) REVERT: C 109 GLU cc_start: 0.8279 (mp0) cc_final: 0.7823 (mp0) REVERT: C 119 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 102 ASP cc_start: 0.7941 (m-30) cc_final: 0.7703 (m-30) REVERT: D 239 SER cc_start: 0.8822 (m) cc_final: 0.8254 (p) REVERT: D 250 ASP cc_start: 0.8180 (t0) cc_final: 0.7894 (t0) REVERT: D 301 SER cc_start: 0.8761 (t) cc_final: 0.8508 (p) REVERT: D 302 PHE cc_start: 0.8751 (m-80) cc_final: 0.8416 (m-80) REVERT: D 306 ASP cc_start: 0.7652 (m-30) cc_final: 0.7152 (m-30) REVERT: D 309 LEU cc_start: 0.8485 (tp) cc_final: 0.8181 (tp) REVERT: D 310 ASP cc_start: 0.7842 (t0) cc_final: 0.7641 (t0) REVERT: D 336 ILE cc_start: 0.8474 (mt) cc_final: 0.8225 (mt) REVERT: D 385 ILE cc_start: 0.8732 (mt) cc_final: 0.8335 (tp) outliers start: 41 outliers final: 25 residues processed: 430 average time/residue: 0.1047 time to fit residues: 58.9396 Evaluate side-chains 446 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 418 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102458 restraints weight = 16428.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106340 restraints weight = 8074.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108956 restraints weight = 4997.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110457 restraints weight = 3554.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111634 restraints weight = 2846.156| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8330 Z= 0.181 Angle : 0.564 7.884 11262 Z= 0.300 Chirality : 0.042 0.242 1332 Planarity : 0.004 0.049 1448 Dihedral : 4.723 45.451 1144 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.85 % Favored : 96.96 % Rotamer: Outliers : 4.83 % Allowed : 26.71 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.27), residues: 1054 helix: 2.37 (0.20), residues: 612 sheet: -0.01 (0.45), residues: 140 loop : -0.39 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 156 TYR 0.018 0.002 TYR B 408 PHE 0.017 0.002 PHE C 170 TRP 0.006 0.001 TRP D 216 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 8330) covalent geometry : angle 0.56400 / 0.30 (11262) hydrogen bonds : bond 0.05882 / 3.99 ( 504) hydrogen bonds : angle 4.33512 / 3.01 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 102 ASP cc_start: 0.7940 (m-30) cc_final: 0.7740 (m-30) REVERT: B 109 ASN cc_start: 0.8625 (t0) cc_final: 0.8322 (t0) REVERT: B 244 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: B 261 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: B 306 ASP cc_start: 0.7588 (m-30) cc_final: 0.7096 (m-30) REVERT: B 328 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8502 (tttt) REVERT: B 347 GLU cc_start: 0.8069 (pm20) cc_final: 0.7696 (pm20) REVERT: B 403 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 410 LEU cc_start: 0.8903 (mp) cc_final: 0.8669 (mm) REVERT: C 89 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8821 (mtmt) REVERT: C 109 GLU cc_start: 0.8274 (mp0) cc_final: 0.7829 (mp0) REVERT: C 154 LYS cc_start: 0.8576 (tttt) cc_final: 0.8262 (tttt) REVERT: C 167 LEU cc_start: 0.9196 (mp) cc_final: 0.8964 (mm) REVERT: D 102 ASP cc_start: 0.7910 (m-30) cc_final: 0.7688 (m-30) REVERT: D 126 GLU cc_start: 0.7751 (mp0) cc_final: 0.7523 (mp0) REVERT: D 202 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8701 (p) REVERT: D 239 SER cc_start: 0.8818 (m) cc_final: 0.8184 (p) REVERT: D 250 ASP cc_start: 0.8244 (t0) cc_final: 0.7865 (t0) REVERT: D 301 SER cc_start: 0.8717 (t) cc_final: 0.8489 (p) REVERT: D 306 ASP cc_start: 0.7651 (m-30) cc_final: 0.7149 (m-30) REVERT: D 309 LEU cc_start: 0.8512 (tp) cc_final: 0.8203 (tp) REVERT: D 347 GLU cc_start: 0.7939 (mp0) cc_final: 0.7340 (mp0) REVERT: D 385 ILE cc_start: 0.8727 (mt) cc_final: 0.8390 (tp) outliers start: 43 outliers final: 24 residues processed: 430 average time/residue: 0.1057 time to fit residues: 59.5726 Evaluate side-chains 443 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 415 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 344 GLN C 234 ASN D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.131395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104781 restraints weight = 16753.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108769 restraints weight = 8186.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111318 restraints weight = 5067.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113169 restraints weight = 3611.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114288 restraints weight = 2823.929| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8330 Z= 0.117 Angle : 0.527 8.010 11262 Z= 0.274 Chirality : 0.040 0.254 1332 Planarity : 0.004 0.053 1448 Dihedral : 4.342 41.443 1142 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.75 % Favored : 97.06 % Rotamer: Outliers : 5.16 % Allowed : 26.60 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.04 (0.27), residues: 1054 helix: 2.52 (0.21), residues: 614 sheet: 0.07 (0.45), residues: 140 loop : -0.49 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 374 TYR 0.017 0.001 TYR B 263 PHE 0.014 0.001 PHE C 170 TRP 0.005 0.001 TRP D 216 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 8330) covalent geometry : angle 0.52669 / 0.27 (11262) hydrogen bonds : bond 0.04406 / 3.01 ( 504) hydrogen bonds : angle 3.91202 / 2.73 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 426 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 119 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 154 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8316 (mtpt) REVERT: A 156 ARG cc_start: 0.8539 (ttt180) cc_final: 0.8268 (ttt-90) REVERT: B 102 ASP cc_start: 0.7939 (m-30) cc_final: 0.7737 (m-30) REVERT: B 109 ASN cc_start: 0.8601 (t0) cc_final: 0.8399 (t0) REVERT: B 244 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: B 247 THR cc_start: 0.8549 (p) cc_final: 0.8277 (t) REVERT: B 261 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8098 (mtpp) REVERT: B 306 ASP cc_start: 0.7530 (m-30) cc_final: 0.7031 (m-30) REVERT: B 317 GLN cc_start: 0.7989 (mt0) cc_final: 0.7718 (mt0) REVERT: B 347 GLU cc_start: 0.8055 (pm20) cc_final: 0.7688 (pm20) REVERT: B 403 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 410 LEU cc_start: 0.8894 (mp) cc_final: 0.8662 (mm) REVERT: C 89 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8814 (mtmt) REVERT: C 109 GLU cc_start: 0.8253 (mp0) cc_final: 0.7817 (mp0) REVERT: C 119 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7997 (mt-10) REVERT: C 154 LYS cc_start: 0.8535 (tttt) cc_final: 0.8201 (tttt) REVERT: C 167 LEU cc_start: 0.9163 (mp) cc_final: 0.8943 (mm) REVERT: C 214 ASP cc_start: 0.6971 (m-30) cc_final: 0.6748 (m-30) REVERT: D 99 VAL cc_start: 0.8792 (p) cc_final: 0.8508 (p) REVERT: D 102 ASP cc_start: 0.7908 (m-30) cc_final: 0.7702 (m-30) REVERT: D 106 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8545 (tp) REVERT: D 196 GLN cc_start: 0.7830 (mm110) cc_final: 0.7493 (mm110) REVERT: D 202 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8669 (p) REVERT: D 239 SER cc_start: 0.8691 (m) cc_final: 0.8185 (t) REVERT: D 250 ASP cc_start: 0.8214 (t0) cc_final: 0.7764 (t0) REVERT: D 261 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8230 (mtpp) REVERT: D 285 THR cc_start: 0.8910 (p) cc_final: 0.8630 (m) REVERT: D 301 SER cc_start: 0.8673 (t) cc_final: 0.8456 (p) REVERT: D 306 ASP cc_start: 0.7610 (m-30) cc_final: 0.7089 (m-30) REVERT: D 309 LEU cc_start: 0.8458 (tp) cc_final: 0.8134 (tp) REVERT: D 347 GLU cc_start: 0.7866 (mp0) cc_final: 0.7267 (mp0) REVERT: D 365 LEU cc_start: 0.8984 (tp) cc_final: 0.8745 (tp) REVERT: D 385 ILE cc_start: 0.8677 (mt) cc_final: 0.8387 (tp) REVERT: D 401 THR cc_start: 0.9075 (p) cc_final: 0.8869 (t) outliers start: 46 outliers final: 25 residues processed: 433 average time/residue: 0.1005 time to fit residues: 57.3418 Evaluate side-chains 443 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 414 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 100.0000 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 290 GLN C 234 ASN D 162 GLN D 220 ASN D 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100747 restraints weight = 16587.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104503 restraints weight = 8086.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106975 restraints weight = 4996.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108734 restraints weight = 3563.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109647 restraints weight = 2800.459| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8330 Z= 0.252 Angle : 0.608 8.184 11262 Z= 0.322 Chirality : 0.043 0.223 1332 Planarity : 0.004 0.050 1448 Dihedral : 4.583 41.264 1140 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.61 % Favored : 96.20 % Rotamer: Outliers : 5.50 % Allowed : 29.18 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.27), residues: 1054 helix: 2.41 (0.21), residues: 610 sheet: 0.11 (0.46), residues: 140 loop : -0.48 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 156 TYR 0.024 0.002 TYR B 263 PHE 0.021 0.002 PHE A 104 TRP 0.007 0.001 TRP C 142 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.25 ( 8330) covalent geometry : angle 0.60816 / 0.32 (11262) hydrogen bonds : bond 0.06156 / 4.12 ( 504) hydrogen bonds : angle 4.26057 / 2.96 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 119 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 154 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8353 (mtpt) REVERT: A 169 ASP cc_start: 0.7459 (m-30) cc_final: 0.7233 (m-30) REVERT: B 102 ASP cc_start: 0.7917 (m-30) cc_final: 0.7714 (m-30) REVERT: B 106 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8542 (tp) REVERT: B 107 ASN cc_start: 0.8459 (t0) cc_final: 0.8249 (t0) REVERT: B 244 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8036 (tp40) REVERT: B 247 THR cc_start: 0.8583 (p) cc_final: 0.8285 (t) REVERT: B 306 ASP cc_start: 0.7599 (m-30) cc_final: 0.7074 (m-30) REVERT: B 317 GLN cc_start: 0.8050 (mt0) cc_final: 0.7773 (mt0) REVERT: B 328 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8492 (tttt) REVERT: B 347 GLU cc_start: 0.8108 (pm20) cc_final: 0.7777 (pm20) REVERT: B 373 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8633 (mmmm) REVERT: B 403 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 410 LEU cc_start: 0.8917 (mp) cc_final: 0.8678 (mm) REVERT: C 89 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8776 (mtmt) REVERT: C 109 GLU cc_start: 0.8304 (mp0) cc_final: 0.7833 (mp0) REVERT: C 119 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 154 LYS cc_start: 0.8571 (tttt) cc_final: 0.8234 (tttt) REVERT: C 167 LEU cc_start: 0.9231 (mp) cc_final: 0.8994 (mm) REVERT: C 229 ASN cc_start: 0.8349 (m-40) cc_final: 0.8074 (m-40) REVERT: D 102 ASP cc_start: 0.7900 (m-30) cc_final: 0.7697 (m-30) REVERT: D 192 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6688 (mt-10) REVERT: D 196 GLN cc_start: 0.7908 (mm110) cc_final: 0.7477 (mm110) REVERT: D 202 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8728 (p) REVERT: D 239 SER cc_start: 0.8822 (m) cc_final: 0.8210 (p) REVERT: D 242 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8701 (tp) REVERT: D 250 ASP cc_start: 0.8297 (t0) cc_final: 0.7895 (t0) REVERT: D 301 SER cc_start: 0.8791 (t) cc_final: 0.8526 (p) REVERT: D 306 ASP cc_start: 0.7682 (m-30) cc_final: 0.7154 (m-30) REVERT: D 309 LEU cc_start: 0.8519 (tp) cc_final: 0.8229 (tp) REVERT: D 336 ILE cc_start: 0.8570 (mt) cc_final: 0.8322 (mt) REVERT: D 347 GLU cc_start: 0.7978 (mp0) cc_final: 0.7389 (mp0) REVERT: D 365 LEU cc_start: 0.8968 (tp) cc_final: 0.8755 (tp) REVERT: D 367 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8460 (m-70) REVERT: D 405 MET cc_start: 0.7959 (tpt) cc_final: 0.7726 (tpt) outliers start: 49 outliers final: 32 residues processed: 444 average time/residue: 0.0991 time to fit residues: 58.0405 Evaluate side-chains 476 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 438 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN C 234 ASN D 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102640 restraints weight = 16377.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106414 restraints weight = 8039.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109065 restraints weight = 4979.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110714 restraints weight = 3517.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111555 restraints weight = 2771.879| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8330 Z= 0.154 Angle : 0.576 7.556 11262 Z= 0.298 Chirality : 0.042 0.277 1332 Planarity : 0.004 0.052 1448 Dihedral : 4.458 39.087 1140 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.85 % Favored : 96.96 % Rotamer: Outliers : 5.16 % Allowed : 30.53 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.15 (0.27), residues: 1054 helix: 2.64 (0.21), residues: 598 sheet: 0.10 (0.47), residues: 140 loop : -0.33 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 374 TYR 0.021 0.002 TYR B 263 PHE 0.034 0.002 PHE D 129 TRP 0.006 0.001 TRP D 216 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8330) covalent geometry : angle 0.57590 / 0.30 (11262) hydrogen bonds : bond 0.05021 / 3.39 ( 504) hydrogen bonds : angle 4.01096 / 2.79 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 438 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 119 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 154 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8354 (mtpt) REVERT: A 169 ASP cc_start: 0.7416 (m-30) cc_final: 0.7174 (m-30) REVERT: A 214 ASP cc_start: 0.6884 (m-30) cc_final: 0.6629 (m-30) REVERT: A 229 ASN cc_start: 0.8080 (m-40) cc_final: 0.7839 (m-40) REVERT: B 102 ASP cc_start: 0.7919 (m-30) cc_final: 0.7710 (m-30) REVERT: B 106 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 107 ASN cc_start: 0.8422 (t0) cc_final: 0.8199 (t0) REVERT: B 118 ASN cc_start: 0.7465 (t0) cc_final: 0.7235 (t0) REVERT: B 244 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: B 247 THR cc_start: 0.8535 (p) cc_final: 0.8261 (t) REVERT: B 306 ASP cc_start: 0.7560 (m-30) cc_final: 0.7036 (m-30) REVERT: B 317 GLN cc_start: 0.8037 (mt0) cc_final: 0.7748 (mt0) REVERT: B 328 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8487 (tttt) REVERT: B 347 GLU cc_start: 0.8062 (pm20) cc_final: 0.7586 (pm20) REVERT: B 403 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 410 LEU cc_start: 0.8905 (mp) cc_final: 0.8662 (mm) REVERT: C 89 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8789 (mtmt) REVERT: C 109 GLU cc_start: 0.8273 (mp0) cc_final: 0.7818 (mp0) REVERT: C 119 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 154 LYS cc_start: 0.8554 (tttt) cc_final: 0.8220 (tttt) REVERT: C 167 LEU cc_start: 0.9227 (mp) cc_final: 0.8989 (mm) REVERT: C 229 ASN cc_start: 0.8315 (m-40) cc_final: 0.8040 (m-40) REVERT: D 102 ASP cc_start: 0.7916 (m-30) cc_final: 0.7707 (m-30) REVERT: D 196 GLN cc_start: 0.7891 (mm110) cc_final: 0.7507 (mm110) REVERT: D 202 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8686 (p) REVERT: D 239 SER cc_start: 0.8739 (m) cc_final: 0.8172 (p) REVERT: D 250 ASP cc_start: 0.8303 (t0) cc_final: 0.7893 (t0) REVERT: D 289 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7416 (mm-30) REVERT: D 301 SER cc_start: 0.8767 (t) cc_final: 0.8508 (p) REVERT: D 302 PHE cc_start: 0.8719 (m-80) cc_final: 0.8258 (m-80) REVERT: D 306 ASP cc_start: 0.7652 (m-30) cc_final: 0.7113 (m-30) REVERT: D 309 LEU cc_start: 0.8502 (tp) cc_final: 0.8187 (tp) REVERT: D 336 ILE cc_start: 0.8499 (mt) cc_final: 0.8254 (mt) REVERT: D 347 GLU cc_start: 0.7933 (mp0) cc_final: 0.7356 (mp0) REVERT: D 367 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (m-70) REVERT: D 385 ILE cc_start: 0.8694 (mt) cc_final: 0.8394 (tp) outliers start: 46 outliers final: 33 residues processed: 442 average time/residue: 0.1004 time to fit residues: 58.4779 Evaluate side-chains 468 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 430 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0870 chunk 5 optimal weight: 0.0770 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 87 optimal weight: 0.0070 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN D 162 GLN D 195 HIS D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107385 restraints weight = 16613.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111251 restraints weight = 8180.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113896 restraints weight = 5057.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115538 restraints weight = 3582.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116792 restraints weight = 2823.604| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8330 Z= 0.113 Angle : 0.569 6.938 11262 Z= 0.289 Chirality : 0.040 0.266 1332 Planarity : 0.004 0.053 1448 Dihedral : 4.266 37.291 1140 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 4.83 % Allowed : 32.10 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.18 (0.27), residues: 1054 helix: 2.66 (0.21), residues: 604 sheet: 0.44 (0.48), residues: 132 loop : -0.55 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 374 TYR 0.017 0.001 TYR B 263 PHE 0.034 0.001 PHE D 129 TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8330) covalent geometry : angle 0.56949 / 0.29 (11262) hydrogen bonds : bond 0.03732 / 2.54 ( 504) hydrogen bonds : angle 3.72900 / 2.60 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 433 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 119 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 154 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8362 (mtpt) REVERT: A 164 PHE cc_start: 0.7626 (t80) cc_final: 0.7356 (t80) REVERT: A 169 ASP cc_start: 0.7353 (m-30) cc_final: 0.7102 (m-30) REVERT: A 214 ASP cc_start: 0.6865 (m-30) cc_final: 0.6632 (m-30) REVERT: B 102 ASP cc_start: 0.7943 (m-30) cc_final: 0.7741 (m-30) REVERT: B 118 ASN cc_start: 0.7264 (t0) cc_final: 0.6977 (t0) REVERT: B 175 SER cc_start: 0.8262 (p) cc_final: 0.7989 (p) REVERT: B 230 ILE cc_start: 0.8711 (mm) cc_final: 0.8266 (mt) REVERT: B 239 SER cc_start: 0.8720 (m) cc_final: 0.8164 (p) REVERT: B 244 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: B 247 THR cc_start: 0.8508 (p) cc_final: 0.8245 (t) REVERT: B 306 ASP cc_start: 0.7482 (m-30) cc_final: 0.6986 (m-30) REVERT: B 317 GLN cc_start: 0.8002 (mt0) cc_final: 0.7714 (mt0) REVERT: B 347 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: B 403 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7497 (mt-10) REVERT: C 89 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8804 (mtmt) REVERT: C 109 GLU cc_start: 0.8242 (mp0) cc_final: 0.7808 (mp0) REVERT: C 119 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7903 (mt-10) REVERT: C 154 LYS cc_start: 0.8528 (tttt) cc_final: 0.8188 (tttt) REVERT: C 167 LEU cc_start: 0.9179 (mp) cc_final: 0.8942 (mm) REVERT: C 229 ASN cc_start: 0.8216 (m-40) cc_final: 0.7952 (m-40) REVERT: D 99 VAL cc_start: 0.8727 (p) cc_final: 0.8467 (p) REVERT: D 102 ASP cc_start: 0.7917 (m-30) cc_final: 0.7673 (m-30) REVERT: D 202 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8622 (p) REVERT: D 209 PHE cc_start: 0.8955 (t80) cc_final: 0.8573 (t80) REVERT: D 239 SER cc_start: 0.8539 (m) cc_final: 0.7996 (t) REVERT: D 242 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8270 (tp) REVERT: D 250 ASP cc_start: 0.8244 (t0) cc_final: 0.7839 (t0) REVERT: D 275 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8201 (ttm170) REVERT: D 289 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7166 (mm-30) REVERT: D 301 SER cc_start: 0.8671 (t) cc_final: 0.8449 (p) REVERT: D 302 PHE cc_start: 0.8664 (m-80) cc_final: 0.8162 (m-80) REVERT: D 306 ASP cc_start: 0.7550 (m-30) cc_final: 0.7034 (m-30) REVERT: D 309 LEU cc_start: 0.8393 (tp) cc_final: 0.8043 (tp) REVERT: D 336 ILE cc_start: 0.8427 (mt) cc_final: 0.8213 (mt) REVERT: D 347 GLU cc_start: 0.7903 (mp0) cc_final: 0.7333 (mp0) REVERT: D 367 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8392 (m-70) REVERT: D 385 ILE cc_start: 0.8643 (mt) cc_final: 0.8396 (tp) outliers start: 43 outliers final: 31 residues processed: 438 average time/residue: 0.0980 time to fit residues: 56.7346 Evaluate side-chains 464 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 232 GLN C 234 ASN D 109 ASN D 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108950 restraints weight = 16387.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112826 restraints weight = 7958.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115506 restraints weight = 4895.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117197 restraints weight = 3462.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118557 restraints weight = 2710.989| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8330 Z= 0.112 Angle : 0.573 7.237 11262 Z= 0.292 Chirality : 0.040 0.239 1332 Planarity : 0.004 0.055 1448 Dihedral : 4.223 37.158 1140 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 4.71 % Allowed : 33.56 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.15 (0.27), residues: 1054 helix: 2.60 (0.21), residues: 610 sheet: 0.40 (0.48), residues: 132 loop : -0.52 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 374 TYR 0.019 0.001 TYR B 263 PHE 0.021 0.001 PHE D 129 TRP 0.009 0.001 TRP B 216 HIS 0.006 0.001 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8330) covalent geometry : angle 0.57339 / 0.29 (11262) hydrogen bonds : bond 0.03710 / 2.51 ( 504) hydrogen bonds : angle 3.67842 / 2.56 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 433 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 119 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 154 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8178 (mtpt) REVERT: A 158 LYS cc_start: 0.8825 (mttt) cc_final: 0.8558 (mptt) REVERT: A 164 PHE cc_start: 0.7592 (t80) cc_final: 0.7334 (t80) REVERT: A 214 ASP cc_start: 0.6819 (m-30) cc_final: 0.6594 (m-30) REVERT: B 102 ASP cc_start: 0.7933 (m-30) cc_final: 0.7708 (m-30) REVERT: B 118 ASN cc_start: 0.7282 (t0) cc_final: 0.6994 (t0) REVERT: B 175 SER cc_start: 0.8255 (p) cc_final: 0.7989 (p) REVERT: B 230 ILE cc_start: 0.8682 (mm) cc_final: 0.8215 (mt) REVERT: B 244 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8126 (tp40) REVERT: B 247 THR cc_start: 0.8487 (p) cc_final: 0.8207 (t) REVERT: B 306 ASP cc_start: 0.7487 (m-30) cc_final: 0.6982 (m-30) REVERT: B 317 GLN cc_start: 0.8022 (mt0) cc_final: 0.7726 (mt0) REVERT: B 347 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: B 403 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 89 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8787 (mtmt) REVERT: C 109 GLU cc_start: 0.8244 (mp0) cc_final: 0.7815 (mp0) REVERT: C 119 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 154 LYS cc_start: 0.8538 (tttt) cc_final: 0.8194 (tttt) REVERT: C 167 LEU cc_start: 0.9155 (mp) cc_final: 0.8927 (mm) REVERT: D 102 ASP cc_start: 0.7923 (m-30) cc_final: 0.7718 (m-30) REVERT: D 106 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8578 (tp) REVERT: D 202 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8629 (p) REVERT: D 209 PHE cc_start: 0.8941 (t80) cc_final: 0.8589 (t80) REVERT: D 239 SER cc_start: 0.8507 (m) cc_final: 0.7970 (t) REVERT: D 242 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8259 (tp) REVERT: D 250 ASP cc_start: 0.8238 (t0) cc_final: 0.7817 (t0) REVERT: D 275 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8210 (ttm170) REVERT: D 289 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 301 SER cc_start: 0.8662 (t) cc_final: 0.8418 (p) REVERT: D 302 PHE cc_start: 0.8662 (m-80) cc_final: 0.8152 (m-80) REVERT: D 306 ASP cc_start: 0.7539 (m-30) cc_final: 0.7032 (m-30) REVERT: D 309 LEU cc_start: 0.8381 (tp) cc_final: 0.8041 (tp) REVERT: D 336 ILE cc_start: 0.8420 (mt) cc_final: 0.8199 (mt) REVERT: D 347 GLU cc_start: 0.7923 (mp0) cc_final: 0.7362 (mp0) REVERT: D 367 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (m-70) REVERT: D 373 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8515 (mmmt) REVERT: D 385 ILE cc_start: 0.8643 (mt) cc_final: 0.8404 (tp) outliers start: 42 outliers final: 32 residues processed: 438 average time/residue: 0.1008 time to fit residues: 58.1234 Evaluate side-chains 469 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 431 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 311 PHE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 232 GLN C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102999 restraints weight = 16317.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106874 restraints weight = 7959.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109389 restraints weight = 4863.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110902 restraints weight = 3458.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111973 restraints weight = 2763.980| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8330 Z= 0.252 Angle : 0.656 7.121 11262 Z= 0.346 Chirality : 0.044 0.169 1332 Planarity : 0.004 0.053 1448 Dihedral : 4.584 39.495 1140 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 5.27 % Allowed : 33.56 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.27), residues: 1054 helix: 2.42 (0.21), residues: 600 sheet: 0.03 (0.47), residues: 142 loop : -0.37 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 156 TYR 0.024 0.002 TYR B 263 PHE 0.024 0.002 PHE A 104 TRP 0.007 0.001 TRP C 142 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 ( 8330) covalent geometry : angle 0.65611 / 0.35 (11262) hydrogen bonds : bond 0.06104 / 4.08 ( 504) hydrogen bonds : angle 4.20404 / 2.92 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 441 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 119 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 154 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8231 (mtpt) REVERT: A 158 LYS cc_start: 0.8884 (mttt) cc_final: 0.8581 (mptt) REVERT: A 225 ASP cc_start: 0.7248 (m-30) cc_final: 0.6857 (m-30) REVERT: A 229 ASN cc_start: 0.8103 (m-40) cc_final: 0.7861 (m-40) REVERT: B 169 GLU cc_start: 0.7628 (tp30) cc_final: 0.7161 (tp30) REVERT: B 244 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8012 (tp40) REVERT: B 247 THR cc_start: 0.8523 (p) cc_final: 0.8238 (t) REVERT: B 306 ASP cc_start: 0.7607 (m-30) cc_final: 0.7077 (m-30) REVERT: B 317 GLN cc_start: 0.8112 (mt0) cc_final: 0.7796 (mt0) REVERT: B 347 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: B 403 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 89 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8751 (mtmt) REVERT: C 109 GLU cc_start: 0.8264 (mp0) cc_final: 0.7827 (mp0) REVERT: C 119 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8012 (mt-10) REVERT: C 154 LYS cc_start: 0.8553 (tttt) cc_final: 0.8213 (tttt) REVERT: C 167 LEU cc_start: 0.9242 (mp) cc_final: 0.9003 (mm) REVERT: C 229 ASN cc_start: 0.8355 (m-40) cc_final: 0.8070 (m-40) REVERT: D 102 ASP cc_start: 0.7925 (m-30) cc_final: 0.7719 (m-30) REVERT: D 192 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7414 (tt0) REVERT: D 196 GLN cc_start: 0.7940 (mm110) cc_final: 0.7585 (mm110) REVERT: D 202 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8750 (p) REVERT: D 222 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 239 SER cc_start: 0.8795 (m) cc_final: 0.8285 (p) REVERT: D 250 ASP cc_start: 0.8344 (t0) cc_final: 0.7942 (t0) REVERT: D 302 PHE cc_start: 0.8755 (m-80) cc_final: 0.8309 (m-80) REVERT: D 306 ASP cc_start: 0.7703 (m-30) cc_final: 0.7158 (m-30) REVERT: D 309 LEU cc_start: 0.8521 (tp) cc_final: 0.8182 (tp) REVERT: D 336 ILE cc_start: 0.8522 (mt) cc_final: 0.8278 (mt) REVERT: D 347 GLU cc_start: 0.7946 (mp0) cc_final: 0.7369 (mp0) REVERT: D 367 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8481 (m-70) REVERT: D 373 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8581 (mmmt) outliers start: 47 outliers final: 33 residues processed: 447 average time/residue: 0.1014 time to fit residues: 59.3180 Evaluate side-chains 474 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 437 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105434 restraints weight = 16223.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109223 restraints weight = 7897.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111830 restraints weight = 4862.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113345 restraints weight = 3443.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114743 restraints weight = 2746.671| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8330 Z= 0.142 Angle : 0.628 6.895 11262 Z= 0.322 Chirality : 0.042 0.149 1332 Planarity : 0.004 0.056 1448 Dihedral : 4.410 37.066 1139 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 3.93 % Allowed : 35.47 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.06 (0.27), residues: 1054 helix: 2.52 (0.21), residues: 596 sheet: 0.38 (0.49), residues: 132 loop : -0.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 374 TYR 0.023 0.002 TYR B 263 PHE 0.028 0.002 PHE D 129 TRP 0.010 0.001 TRP D 216 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 8330) covalent geometry : angle 0.62817 / 0.32 (11262) hydrogen bonds : bond 0.04819 / 3.26 ( 504) hydrogen bonds : angle 3.89754 / 2.69 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 436 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 119 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 154 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8169 (mtpt) REVERT: A 158 LYS cc_start: 0.8875 (mttt) cc_final: 0.8581 (mptt) REVERT: A 164 PHE cc_start: 0.7630 (t80) cc_final: 0.7368 (t80) REVERT: A 225 ASP cc_start: 0.7202 (m-30) cc_final: 0.6813 (m-30) REVERT: A 229 ASN cc_start: 0.8020 (m-40) cc_final: 0.7749 (m-40) REVERT: B 209 PHE cc_start: 0.9002 (t80) cc_final: 0.8750 (t80) REVERT: B 244 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8047 (tp40) REVERT: B 247 THR cc_start: 0.8505 (p) cc_final: 0.8226 (t) REVERT: B 306 ASP cc_start: 0.7531 (m-30) cc_final: 0.7039 (m-30) REVERT: B 317 GLN cc_start: 0.8063 (mt0) cc_final: 0.7751 (mt0) REVERT: B 347 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: B 403 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 89 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8757 (mtmt) REVERT: C 109 GLU cc_start: 0.8260 (mp0) cc_final: 0.7821 (mp0) REVERT: C 119 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7968 (mt-10) REVERT: C 154 LYS cc_start: 0.8526 (tttt) cc_final: 0.8179 (tttt) REVERT: C 167 LEU cc_start: 0.9223 (mp) cc_final: 0.8989 (mm) REVERT: C 229 ASN cc_start: 0.8313 (m-40) cc_final: 0.8045 (m-40) REVERT: D 99 VAL cc_start: 0.8709 (p) cc_final: 0.8509 (p) REVERT: D 102 ASP cc_start: 0.7930 (m-30) cc_final: 0.7687 (m-30) REVERT: D 106 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8580 (tp) REVERT: D 192 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7298 (tt0) REVERT: D 202 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8688 (p) REVERT: D 239 SER cc_start: 0.8713 (m) cc_final: 0.8144 (p) REVERT: D 250 ASP cc_start: 0.8347 (t0) cc_final: 0.7939 (t0) REVERT: D 302 PHE cc_start: 0.8723 (m-80) cc_final: 0.8293 (m-80) REVERT: D 306 ASP cc_start: 0.7640 (m-30) cc_final: 0.7092 (m-30) REVERT: D 309 LEU cc_start: 0.8444 (tp) cc_final: 0.8094 (tp) REVERT: D 336 ILE cc_start: 0.8459 (mt) cc_final: 0.8199 (mt) REVERT: D 347 GLU cc_start: 0.7915 (mp0) cc_final: 0.7352 (mp0) REVERT: D 367 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8452 (m-70) REVERT: D 373 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8560 (mmmt) REVERT: D 385 ILE cc_start: 0.8675 (mt) cc_final: 0.8396 (tp) outliers start: 35 outliers final: 27 residues processed: 439 average time/residue: 0.1044 time to fit residues: 60.1650 Evaluate side-chains 468 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 436 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 367 HIS Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.132167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106212 restraints weight = 16334.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110051 restraints weight = 7953.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112623 restraints weight = 4892.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114482 restraints weight = 3465.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115272 restraints weight = 2690.040| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8330 Z= 0.131 Angle : 0.623 7.136 11262 Z= 0.317 Chirality : 0.041 0.166 1332 Planarity : 0.004 0.055 1448 Dihedral : 4.337 37.224 1139 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 4.26 % Allowed : 35.13 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.00 (0.27), residues: 1054 helix: 2.45 (0.21), residues: 602 sheet: 0.37 (0.49), residues: 132 loop : -0.44 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 374 TYR 0.022 0.001 TYR B 263 PHE 0.025 0.002 PHE D 129 TRP 0.012 0.001 TRP B 216 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8330) covalent geometry : angle 0.62267 / 0.32 (11262) hydrogen bonds : bond 0.04485 / 3.03 ( 504) hydrogen bonds : angle 3.82450 / 2.64 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.39 seconds wall clock time: 33 minutes 5.20 seconds (1985.20 seconds total)