Starting phenix.real_space_refine on Fri Mar 14 05:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.map" model { file = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2025/7p4i_13193.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.023 sd= 0.073 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 48 5.16 5 C 6198 2.51 5 N 1572 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3170 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 6.19, per 1000 atoms: 0.65 Number of scatterers: 9510 At special positions: 0 Unit cell: (120.146, 119.294, 86.9142, 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 48 16.00 O 1692 8.00 N 1572 7.00 C 6198 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: 2.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 79.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.664A pdb=" N ARG A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A 89 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 140 removed outlier: 4.054A pdb=" N ALA A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.109A pdb=" N MET A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.528A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 378 removed outlier: 4.082A pdb=" N THR A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.569A pdb=" N ILE A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP A 444 " --> pdb=" O PRO A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.663A pdb=" N ARG B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.588A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 4.109A pdb=" N MET B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 322 removed outlier: 5.088A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.528A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.570A pdb=" N ILE B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 removed outlier: 4.370A pdb=" N ASP B 444 " --> pdb=" O PRO B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.157A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 480 removed outlier: 3.949A pdb=" N VAL B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.665A pdb=" N ARG C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 223 through 240 removed outlier: 4.258A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 285 removed outlier: 3.997A pdb=" N ILE C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 4.108A pdb=" N MET C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Proline residue: C 314 - end of helix removed outlier: 3.527A pdb=" N PHE C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.870A pdb=" N LEU C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 330' Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.652A pdb=" N CYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 removed outlier: 3.656A pdb=" N ILE C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 427 through 439 removed outlier: 3.568A pdb=" N ILE C 438 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP C 444 " --> pdb=" O PRO C 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 189 through 196 Processing sheet with id=AA3, first strand: chain 'C' and resid 189 through 196 594 hydrogen bonds defined for protein. 1737 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: 3.04 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2999 1.34 - 1.46: 1178 1.46 - 1.57: 5414 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9672 Sorted by residual: bond pdb=" C PHE B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.26e+00 bond pdb=" C PHE C 77 " pdb=" N PRO C 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.12e+00 bond pdb=" C PHE A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" C ALA A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.46e+00 bond pdb=" C ALA C 334 " pdb=" N PRO C 335 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.39e+00 ... (remaining 9667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12834 2.04 - 4.07: 249 4.07 - 6.11: 60 6.11 - 8.15: 9 8.15 - 10.18: 6 Bond angle restraints: 13158 Sorted by residual: angle pdb=" C ALA B 76 " pdb=" N PHE B 77 " pdb=" CA PHE B 77 " ideal model delta sigma weight residual 120.26 124.54 -4.28 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA C 76 " pdb=" N PHE C 77 " pdb=" CA PHE C 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" CA LEU B 313 " pdb=" CB LEU B 313 " pdb=" CG LEU B 313 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" CA LEU C 313 " pdb=" CB LEU C 313 " pdb=" CG LEU C 313 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 ... (remaining 13153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 4786 11.89 - 23.79: 625 23.79 - 35.68: 226 35.68 - 47.57: 57 47.57 - 59.46: 15 Dihedral angle restraints: 5709 sinusoidal: 2082 harmonic: 3627 Sorted by residual: dihedral pdb=" CA LEU B 62 " pdb=" C LEU B 62 " pdb=" N ARG B 63 " pdb=" CA ARG B 63 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU C 62 " pdb=" C LEU C 62 " pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual -180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1018 0.032 - 0.064: 460 0.064 - 0.096: 137 0.096 - 0.128: 41 0.128 - 0.160: 3 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU C 313 " pdb=" N LEU C 313 " pdb=" C LEU C 313 " pdb=" CB LEU C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA LEU A 313 " pdb=" N LEU A 313 " pdb=" C LEU A 313 " pdb=" CB LEU A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA LEU B 313 " pdb=" N LEU B 313 " pdb=" C LEU B 313 " pdb=" CB LEU B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 1656 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO B 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " -0.022 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 364 2.71 - 3.26: 10712 3.26 - 3.81: 15044 3.81 - 4.35: 18140 4.35 - 4.90: 28741 Nonbonded interactions: 73001 Sorted by model distance: nonbonded pdb=" O VAL B 260 " pdb=" OG SER B 263 " model vdw 2.168 3.040 nonbonded pdb=" O VAL A 260 " pdb=" OG SER A 263 " model vdw 2.168 3.040 nonbonded pdb=" O VAL C 260 " pdb=" OG SER C 263 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR C 167 " pdb=" OH TYR C 195 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 167 " pdb=" OH TYR A 195 " model vdw 2.232 3.040 ... (remaining 72996 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.370 Find NCS groups from input model: 0.180 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9672 Z= 0.179 Angle : 0.765 10.183 13158 Z= 0.410 Chirality : 0.039 0.160 1659 Planarity : 0.004 0.039 1626 Dihedral : 13.104 59.464 3381 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1272 helix: 0.56 (0.19), residues: 780 sheet: -2.19 (0.48), residues: 48 loop : -1.74 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 267 HIS 0.004 0.001 HIS C 476 PHE 0.007 0.001 PHE C 250 TYR 0.011 0.001 TYR A 191 ARG 0.003 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.006 Fit side-chains REVERT: A 85 MET cc_start: 0.8983 (mtm) cc_final: 0.8667 (ptp) REVERT: A 266 MET cc_start: 0.9299 (mmm) cc_final: 0.8939 (mmm) REVERT: B 85 MET cc_start: 0.9152 (mtm) cc_final: 0.8852 (mtm) REVERT: C 221 MET cc_start: 0.8992 (ptp) cc_final: 0.8637 (ptp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1901 time to fit residues: 10.3194 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.031114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025441 restraints weight = 162835.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026114 restraints weight = 87708.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.026579 restraints weight = 57356.883| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9672 Z= 0.210 Angle : 0.643 8.896 13158 Z= 0.327 Chirality : 0.040 0.143 1659 Planarity : 0.004 0.037 1626 Dihedral : 4.678 29.954 1344 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.29 % Allowed : 9.34 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1272 helix: 0.83 (0.19), residues: 804 sheet: -1.94 (0.54), residues: 48 loop : -1.83 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 267 HIS 0.003 0.001 HIS A 476 PHE 0.011 0.001 PHE A 250 TYR 0.010 0.002 TYR A 268 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 1.142 Fit side-chains REVERT: A 85 MET cc_start: 0.8969 (mtm) cc_final: 0.8638 (ptp) REVERT: A 266 MET cc_start: 0.9116 (mmm) cc_final: 0.8827 (mmm) REVERT: C 88 MET cc_start: 0.8805 (mmt) cc_final: 0.8510 (tpp) REVERT: C 266 MET cc_start: 0.9156 (mmm) cc_final: 0.8833 (mmm) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.1819 time to fit residues: 10.9354 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 50.0000 chunk 31 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 0.0980 chunk 22 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 50.0000 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.031394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.025755 restraints weight = 163619.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026440 restraints weight = 87189.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.026918 restraints weight = 56860.528| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9672 Z= 0.155 Angle : 0.661 9.479 13158 Z= 0.321 Chirality : 0.041 0.153 1659 Planarity : 0.004 0.035 1626 Dihedral : 4.475 28.377 1344 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1272 helix: 0.97 (0.19), residues: 801 sheet: -1.85 (0.50), residues: 48 loop : -1.56 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 453 HIS 0.002 0.001 HIS B 475 PHE 0.023 0.001 PHE A 250 TYR 0.011 0.001 TYR B 191 ARG 0.004 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.025 Fit side-chains REVERT: A 85 MET cc_start: 0.8985 (mtm) cc_final: 0.8654 (ptp) REVERT: B 85 MET cc_start: 0.9010 (mtm) cc_final: 0.8579 (ptp) REVERT: B 259 MET cc_start: 0.8882 (tmm) cc_final: 0.8681 (tmm) REVERT: C 221 MET cc_start: 0.9165 (ptp) cc_final: 0.8775 (ptp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1904 time to fit residues: 10.5431 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 20.0000 chunk 23 optimal weight: 0.0570 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.036052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.026867 restraints weight = 128243.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.027457 restraints weight = 88880.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027866 restraints weight = 68850.325| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9672 Z= 0.196 Angle : 0.636 8.471 13158 Z= 0.318 Chirality : 0.040 0.148 1659 Planarity : 0.003 0.030 1626 Dihedral : 4.510 27.652 1344 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1272 helix: 1.05 (0.19), residues: 801 sheet: -2.13 (0.48), residues: 48 loop : -1.53 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 264 HIS 0.003 0.001 HIS B 475 PHE 0.018 0.001 PHE A 250 TYR 0.008 0.001 TYR A 74 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.857 Fit side-chains REVERT: A 85 MET cc_start: 0.8883 (mtm) cc_final: 0.8656 (ptp) REVERT: A 379 MET cc_start: 0.8840 (ptp) cc_final: 0.8372 (mpp) REVERT: B 85 MET cc_start: 0.8861 (mtm) cc_final: 0.8481 (ptp) REVERT: B 259 MET cc_start: 0.8817 (tmm) cc_final: 0.8612 (tmm) REVERT: C 88 MET cc_start: 0.8660 (mmt) cc_final: 0.8388 (tpp) REVERT: C 379 MET cc_start: 0.8927 (ptp) cc_final: 0.8322 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1923 time to fit residues: 10.5263 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.035888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.026861 restraints weight = 129257.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027452 restraints weight = 88618.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.027894 restraints weight = 68285.371| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9672 Z= 0.155 Angle : 0.652 8.949 13158 Z= 0.316 Chirality : 0.040 0.149 1659 Planarity : 0.003 0.028 1626 Dihedral : 4.404 26.103 1344 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1272 helix: 1.05 (0.19), residues: 804 sheet: -2.02 (0.48), residues: 48 loop : -1.39 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 453 HIS 0.002 0.001 HIS B 475 PHE 0.020 0.001 PHE A 250 TYR 0.009 0.001 TYR B 191 ARG 0.001 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.067 Fit side-chains REVERT: A 81 MET cc_start: 0.9682 (mmt) cc_final: 0.9379 (mmm) REVERT: A 85 MET cc_start: 0.8900 (mtm) cc_final: 0.8664 (ptp) REVERT: A 379 MET cc_start: 0.8818 (ptp) cc_final: 0.8341 (mpp) REVERT: B 85 MET cc_start: 0.8814 (mtm) cc_final: 0.8587 (ptp) REVERT: B 266 MET cc_start: 0.9089 (mmm) cc_final: 0.8841 (mmm) REVERT: B 274 MET cc_start: 0.9488 (ppp) cc_final: 0.9282 (ppp) REVERT: C 266 MET cc_start: 0.9152 (mmm) cc_final: 0.8799 (mmm) REVERT: C 274 MET cc_start: 0.9541 (ppp) cc_final: 0.9327 (ppp) REVERT: C 379 MET cc_start: 0.8894 (ptp) cc_final: 0.8260 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2004 time to fit residues: 11.4209 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 47 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.026019 restraints weight = 160858.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.026540 restraints weight = 97790.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.026916 restraints weight = 68917.226| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9672 Z= 0.150 Angle : 0.673 9.392 13158 Z= 0.321 Chirality : 0.040 0.155 1659 Planarity : 0.004 0.052 1626 Dihedral : 4.380 27.993 1344 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1272 helix: 1.14 (0.19), residues: 813 sheet: -2.60 (0.49), residues: 60 loop : -1.20 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 453 HIS 0.002 0.001 HIS C 308 PHE 0.020 0.001 PHE A 250 TYR 0.009 0.001 TYR B 191 ARG 0.007 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.014 Fit side-chains REVERT: A 81 MET cc_start: 0.9673 (mmt) cc_final: 0.9352 (mmm) REVERT: A 85 MET cc_start: 0.8866 (mtm) cc_final: 0.8650 (ptp) REVERT: A 379 MET cc_start: 0.8747 (ptp) cc_final: 0.8235 (mpp) REVERT: B 81 MET cc_start: 0.9667 (mmt) cc_final: 0.9393 (mmm) REVERT: B 85 MET cc_start: 0.8858 (mtm) cc_final: 0.8504 (ptp) REVERT: B 88 MET cc_start: 0.8644 (mmt) cc_final: 0.8424 (tpp) REVERT: B 274 MET cc_start: 0.9361 (ppp) cc_final: 0.9154 (ppp) REVERT: B 353 MET cc_start: 0.8991 (ptp) cc_final: 0.8360 (pmm) REVERT: C 88 MET cc_start: 0.8729 (mmt) cc_final: 0.8428 (tpp) REVERT: C 221 MET cc_start: 0.9101 (ptp) cc_final: 0.8735 (ptp) REVERT: C 266 MET cc_start: 0.9086 (mmm) cc_final: 0.8815 (mmm) REVERT: C 353 MET cc_start: 0.9035 (ptp) cc_final: 0.8518 (pmm) REVERT: C 379 MET cc_start: 0.8784 (ptp) cc_final: 0.8213 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1820 time to fit residues: 9.9658 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.0020 chunk 79 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.035675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026543 restraints weight = 129901.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.027128 restraints weight = 89380.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027552 restraints weight = 68827.348| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9672 Z= 0.226 Angle : 0.670 8.117 13158 Z= 0.334 Chirality : 0.041 0.155 1659 Planarity : 0.003 0.028 1626 Dihedral : 4.522 28.819 1344 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1272 helix: 1.18 (0.19), residues: 807 sheet: -2.73 (0.50), residues: 60 loop : -1.05 (0.35), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 267 HIS 0.004 0.001 HIS C 475 PHE 0.014 0.001 PHE A 250 TYR 0.008 0.001 TYR A 74 ARG 0.005 0.001 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.140 Fit side-chains REVERT: A 81 MET cc_start: 0.9689 (mmt) cc_final: 0.9430 (mmm) REVERT: A 85 MET cc_start: 0.8892 (mtm) cc_final: 0.8668 (ptp) REVERT: A 274 MET cc_start: 0.9495 (ppp) cc_final: 0.9249 (ppp) REVERT: A 379 MET cc_start: 0.8862 (ptp) cc_final: 0.8303 (mpp) REVERT: B 81 MET cc_start: 0.9664 (mmt) cc_final: 0.9406 (mmm) REVERT: B 85 MET cc_start: 0.8896 (mtm) cc_final: 0.8608 (ptp) REVERT: C 88 MET cc_start: 0.8802 (mmt) cc_final: 0.8515 (tpp) REVERT: C 266 MET cc_start: 0.9110 (mmm) cc_final: 0.8873 (mmm) REVERT: C 379 MET cc_start: 0.8880 (ptp) cc_final: 0.8276 (mpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2255 time to fit residues: 13.3376 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 397 ASN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.030779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025643 restraints weight = 163411.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.026174 restraints weight = 99748.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.026556 restraints weight = 70551.094| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9672 Z= 0.158 Angle : 0.667 9.160 13158 Z= 0.324 Chirality : 0.041 0.160 1659 Planarity : 0.003 0.025 1626 Dihedral : 4.446 29.484 1344 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 807 sheet: -2.66 (0.51), residues: 60 loop : -0.95 (0.35), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 453 HIS 0.002 0.001 HIS C 308 PHE 0.019 0.001 PHE A 250 TYR 0.008 0.001 TYR B 191 ARG 0.003 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.184 Fit side-chains REVERT: A 81 MET cc_start: 0.9716 (mmt) cc_final: 0.9432 (mmm) REVERT: A 85 MET cc_start: 0.8909 (mtm) cc_final: 0.8695 (ptp) REVERT: A 353 MET cc_start: 0.8998 (ptp) cc_final: 0.8329 (pmm) REVERT: A 379 MET cc_start: 0.8749 (ptp) cc_final: 0.8217 (mpp) REVERT: B 81 MET cc_start: 0.9705 (mmt) cc_final: 0.9432 (mmm) REVERT: B 85 MET cc_start: 0.8915 (mtm) cc_final: 0.8660 (ptp) REVERT: B 274 MET cc_start: 0.9382 (ppp) cc_final: 0.9088 (ppp) REVERT: B 353 MET cc_start: 0.8987 (ptp) cc_final: 0.8261 (pmm) REVERT: B 379 MET cc_start: 0.8869 (ptp) cc_final: 0.8402 (mpp) REVERT: C 266 MET cc_start: 0.9055 (mmm) cc_final: 0.8791 (mmm) REVERT: C 353 MET cc_start: 0.8802 (ptp) cc_final: 0.8101 (pmm) REVERT: C 379 MET cc_start: 0.8820 (ptp) cc_final: 0.8230 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2677 time to fit residues: 13.9383 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 29 optimal weight: 0.0970 chunk 14 optimal weight: 40.0000 chunk 76 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.035653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.026781 restraints weight = 129095.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027356 restraints weight = 89152.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.027769 restraints weight = 68981.953| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9672 Z= 0.154 Angle : 0.667 10.111 13158 Z= 0.319 Chirality : 0.040 0.157 1659 Planarity : 0.003 0.024 1626 Dihedral : 4.370 28.958 1344 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 816 sheet: -2.63 (0.51), residues: 60 loop : -0.99 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 264 HIS 0.001 0.001 HIS C 308 PHE 0.018 0.001 PHE A 250 TYR 0.007 0.001 TYR C 74 ARG 0.003 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.025 Fit side-chains REVERT: A 81 MET cc_start: 0.9674 (mmt) cc_final: 0.9354 (mmm) REVERT: A 274 MET cc_start: 0.9443 (ppp) cc_final: 0.9239 (ppp) REVERT: A 353 MET cc_start: 0.8942 (ptp) cc_final: 0.8367 (pmm) REVERT: B 221 MET cc_start: 0.9003 (ptp) cc_final: 0.8699 (ptp) REVERT: B 353 MET cc_start: 0.8928 (ptp) cc_final: 0.8225 (pmm) REVERT: B 379 MET cc_start: 0.8916 (ptp) cc_final: 0.8390 (mpp) REVERT: C 221 MET cc_start: 0.8940 (ptp) cc_final: 0.8603 (ptp) REVERT: C 353 MET cc_start: 0.8720 (ptp) cc_final: 0.8105 (pmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1888 time to fit residues: 10.4768 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.030873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.025786 restraints weight = 163893.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.026301 restraints weight = 100379.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.026658 restraints weight = 70848.927| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9672 Z= 0.154 Angle : 0.672 9.714 13158 Z= 0.322 Chirality : 0.040 0.156 1659 Planarity : 0.003 0.024 1626 Dihedral : 4.360 29.037 1344 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 816 sheet: -2.58 (0.51), residues: 60 loop : -0.95 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 453 HIS 0.002 0.001 HIS C 308 PHE 0.018 0.001 PHE A 250 TYR 0.007 0.001 TYR C 191 ARG 0.002 0.000 ARG C 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.094 Fit side-chains REVERT: A 353 MET cc_start: 0.8990 (ptp) cc_final: 0.8311 (pmm) REVERT: A 379 MET cc_start: 0.8887 (ptp) cc_final: 0.8393 (mpp) REVERT: B 221 MET cc_start: 0.9195 (ptp) cc_final: 0.8905 (ptp) REVERT: B 353 MET cc_start: 0.9026 (ptp) cc_final: 0.8037 (pmm) REVERT: B 379 MET cc_start: 0.8835 (ptp) cc_final: 0.8374 (mpp) REVERT: C 85 MET cc_start: 0.8934 (ptp) cc_final: 0.8717 (ptp) REVERT: C 221 MET cc_start: 0.9116 (ptp) cc_final: 0.8750 (ptp) REVERT: C 353 MET cc_start: 0.8799 (ptp) cc_final: 0.8124 (pmm) REVERT: C 379 MET cc_start: 0.8857 (ptp) cc_final: 0.8390 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1872 time to fit residues: 10.2389 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 chunk 57 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.030333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.025013 restraints weight = 164720.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.025584 restraints weight = 95282.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026000 restraints weight = 65232.749| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9672 Z= 0.224 Angle : 0.691 9.805 13158 Z= 0.344 Chirality : 0.041 0.154 1659 Planarity : 0.003 0.022 1626 Dihedral : 4.606 30.231 1344 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1272 helix: 1.17 (0.18), residues: 816 sheet: -2.73 (0.51), residues: 60 loop : -0.90 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 267 HIS 0.005 0.001 HIS B 475 PHE 0.013 0.001 PHE A 250 TYR 0.022 0.001 TYR C 74 ARG 0.003 0.000 ARG C 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.26 seconds wall clock time: 50 minutes 4.48 seconds (3004.48 seconds total)