Starting phenix.real_space_refine on Wed Aug 5 22:59:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993.map" model { file = "/net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ve1_64993/08_2026/9ve1_64993_neut_trim.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 57 5.16 5 C 7845 2.51 5 N 1866 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3925 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "B" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3925 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "C" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3925 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.25 Number of scatterers: 11796 At special positions: 0 Unit cell: (92.421, 109.431, 122.472, 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 57 16.00 O 2028 8.00 N 1866 7.00 C 7845 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: 0.89 Conformation dependent library (CDL) restraints added in 611.7 milliseconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.829A pdb=" N TYR A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.568A pdb=" N LEU A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.656A pdb=" N TYR A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.519A pdb=" N SER A 79 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.868A pdb=" N LEU A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.612A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.874A pdb=" N MET A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.836A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.726A pdb=" N SER A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 187 removed outlier: 3.805A pdb=" N ASN A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 188 through 225 removed outlier: 3.846A pdb=" N ALA A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 removed outlier: 3.717A pdb=" N ILE A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 257 through 279 removed outlier: 4.209A pdb=" N VAL A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.810A pdb=" N ASN A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.547A pdb=" N ASN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.535A pdb=" N TRP A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.774A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 356 removed outlier: 3.875A pdb=" N ILE A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.731A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS A 379 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.843A pdb=" N GLU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.865A pdb=" N LEU A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 435 removed outlier: 3.917A pdb=" N SER A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 469 removed outlier: 3.586A pdb=" N ARG A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.740A pdb=" N LEU A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 512 removed outlier: 3.972A pdb=" N PHE A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 35 removed outlier: 3.503A pdb=" N THR B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.568A pdb=" N LEU B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.656A pdb=" N TYR B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.519A pdb=" N SER B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.510A pdb=" N MET B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 4.054A pdb=" N LEU B 109 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.611A pdb=" N VAL B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.875A pdb=" N MET B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 145 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.836A pdb=" N MET B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.726A pdb=" N SER B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.807A pdb=" N ASN B 187 " --> pdb=" O LYS B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 188 through 225 removed outlier: 3.846A pdb=" N ALA B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 251 removed outlier: 3.716A pdb=" N ILE B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 257 through 279 removed outlier: 4.210A pdb=" N VAL B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.811A pdb=" N ASN B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.600A pdb=" N ASN B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.536A pdb=" N TRP B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.773A pdb=" N LEU B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.875A pdb=" N ILE B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.730A pdb=" N PHE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.842A pdb=" N GLU B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.865A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 435 removed outlier: 3.917A pdb=" N SER B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 removed outlier: 3.587A pdb=" N ARG B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.741A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 512 removed outlier: 3.972A pdb=" N PHE B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 removed outlier: 3.590A pdb=" N TYR C 19 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.568A pdb=" N LEU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 74 removed outlier: 3.656A pdb=" N TYR C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.519A pdb=" N SER C 79 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.524A pdb=" N ALA C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.868A pdb=" N LEU C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.612A pdb=" N VAL C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.875A pdb=" N MET C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS C 145 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.836A pdb=" N MET C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.726A pdb=" N SER C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 removed outlier: 3.805A pdb=" N ASN C 187 " --> pdb=" O LYS C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 188 through 225 removed outlier: 3.846A pdb=" N ALA C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 251 removed outlier: 3.716A pdb=" N ILE C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 257 through 279 removed outlier: 4.211A pdb=" N VAL C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.811A pdb=" N ASN C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.535A pdb=" N TRP C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.773A pdb=" N LEU C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 removed outlier: 3.875A pdb=" N ILE C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 379 removed outlier: 3.730A pdb=" N PHE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.843A pdb=" N GLU C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.864A pdb=" N LEU C 400 " --> pdb=" O PHE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 435 removed outlier: 3.916A pdb=" N SER C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 412 " --> pdb=" O PHE C 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 469 removed outlier: 3.587A pdb=" N ARG C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.740A pdb=" N LEU C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 512 removed outlier: 3.973A pdb=" N PHE C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN C 511 " --> pdb=" O ARG C 507 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2070 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: 1.95 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3521 1.35 - 1.47: 3313 1.47 - 1.58: 5181 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 12123 Sorted by residual: bond pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.30e+01 bond pdb=" N ILE B 105 " pdb=" CA ILE B 105 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.60e+00 bond pdb=" N VAL A 313 " pdb=" CA VAL A 313 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.48e+00 bond pdb=" N VAL C 313 " pdb=" CA VAL C 313 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.17e-02 7.31e+03 9.11e+00 bond pdb=" N PHE C 91 " pdb=" CA PHE C 91 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.70e+00 ... (remaining 12118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16081 2.24 - 4.48: 368 4.48 - 6.73: 46 6.73 - 8.97: 17 8.97 - 11.21: 9 Bond angle restraints: 16521 Sorted by residual: angle pdb=" N ILE C 341 " pdb=" CA ILE C 341 " pdb=" C ILE C 341 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N PRO B 312 " pdb=" CA PRO B 312 " pdb=" C PRO B 312 " ideal model delta sigma weight residual 112.47 104.49 7.98 2.06e+00 2.36e-01 1.50e+01 angle pdb=" CB GLU A 85 " pdb=" CG GLU A 85 " pdb=" CD GLU A 85 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" CB GLU C 85 " pdb=" CG GLU C 85 " pdb=" CD GLU C 85 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" CB GLU B 85 " pdb=" CG GLU B 85 " pdb=" CD GLU B 85 " ideal model delta sigma weight residual 112.60 119.12 -6.52 1.70e+00 3.46e-01 1.47e+01 ... (remaining 16516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 5955 15.99 - 31.99: 716 31.99 - 47.98: 155 47.98 - 63.97: 38 63.97 - 79.97: 6 Dihedral angle restraints: 6870 sinusoidal: 2547 harmonic: 4323 Sorted by residual: dihedral pdb=" CA ASN B 169 " pdb=" CB ASN B 169 " pdb=" CG ASN B 169 " pdb=" OD1 ASN B 169 " ideal model delta sinusoidal sigma weight residual 120.00 -174.06 -65.94 2 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASN A 169 " pdb=" CB ASN A 169 " pdb=" CG ASN A 169 " pdb=" OD1 ASN A 169 " ideal model delta sinusoidal sigma weight residual 120.00 -174.08 -65.92 2 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASN C 169 " pdb=" CB ASN C 169 " pdb=" CG ASN C 169 " pdb=" OD1 ASN C 169 " ideal model delta sinusoidal sigma weight residual 120.00 -174.09 -65.91 2 2.00e+01 2.50e-03 1.00e+01 ... (remaining 6867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1365 0.042 - 0.084: 424 0.084 - 0.126: 84 0.126 - 0.168: 22 0.168 - 0.210: 4 Chirality restraints: 1899 Sorted by residual: chirality pdb=" CA ILE C 341 " pdb=" N ILE C 341 " pdb=" C ILE C 341 " pdb=" CB ILE C 341 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL B 16 " pdb=" N VAL B 16 " pdb=" C VAL B 16 " pdb=" CB VAL B 16 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 1896 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 333 " 0.016 2.00e-02 2.50e+03 2.71e-02 1.29e+01 pdb=" CG PHE B 333 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 333 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 333 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE B 333 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 333 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 333 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 333 " -0.016 2.00e-02 2.50e+03 2.71e-02 1.29e+01 pdb=" CG PHE A 333 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 333 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 333 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 333 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 333 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 333 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 333 " -0.016 2.00e-02 2.50e+03 2.69e-02 1.27e+01 pdb=" CG PHE C 333 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 333 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 333 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE C 333 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 333 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 333 " 0.001 2.00e-02 2.50e+03 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2314 2.77 - 3.30: 10350 3.30 - 3.84: 18812 3.84 - 4.37: 21537 4.37 - 4.90: 38720 Nonbonded interactions: 91733 Sorted by model distance: nonbonded pdb=" N GLY C 106 " pdb=" O6 CHT C 601 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASP C 108 " pdb=" O6 CHT C 601 " model vdw 2.294 3.040 nonbonded pdb=" OD2 ASP A 108 " pdb=" O6 CHT A 601 " model vdw 2.312 3.040 nonbonded pdb=" O ILE C 458 " pdb=" OG1 THR C 462 " model vdw 2.334 3.040 nonbonded pdb=" O ILE B 458 " pdb=" OG1 THR B 462 " model vdw 2.335 3.040 ... (remaining 91728 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.740 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12123 Z= 0.283 Angle : 0.859 11.208 16521 Z= 0.507 Chirality : 0.043 0.210 1899 Planarity : 0.006 0.113 2016 Dihedral : 14.629 79.967 4110 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.89 % Allowed : 14.19 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.14), residues: 1503 helix: -3.46 (0.09), residues: 1089 sheet: None (None), residues: 0 loop : -1.89 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 345 TYR 0.036 0.002 TYR A 421 PHE 0.061 0.001 PHE A 333 TRP 0.016 0.001 TRP C 324 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.28 (12123) covalent geometry : angle 0.85916 / 0.51 (16521) hydrogen bonds : bond 0.33027 / 21.53 ( 711) hydrogen bonds : angle 9.31640 / 6.51 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 285 time to evaluate : 0.474 Fit side-chains REVERT: A 19 TYR cc_start: 0.7997 (m-80) cc_final: 0.7685 (m-80) REVERT: A 48 ASP cc_start: 0.7715 (t0) cc_final: 0.7171 (t0) REVERT: A 93 LEU cc_start: 0.7055 (pt) cc_final: 0.6614 (pt) REVERT: B 36 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7502 (mtp-110) REVERT: B 131 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7768 (p) REVERT: B 386 GLU cc_start: 0.8208 (tp30) cc_final: 0.7498 (pp20) REVERT: B 438 GLN cc_start: 0.7317 (tt0) cc_final: 0.6904 (tp40) REVERT: B 442 ILE cc_start: 0.8860 (pt) cc_final: 0.8518 (mp) REVERT: C 76 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.6805 (mtm-85) REVERT: C 210 LEU cc_start: 0.8718 (tp) cc_final: 0.8202 (mm) REVERT: C 420 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6641 (t80) REVERT: C 465 MET cc_start: 0.8532 (tpp) cc_final: 0.8271 (mmm) outliers start: 11 outliers final: 0 residues processed: 293 average time/residue: 0.1058 time to fit residues: 45.4584 Evaluate side-chains 188 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 420 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 187 ASN B 291 ASN B 371 ASN B 391 HIS B 443 ASN C 291 ASN C 371 ASN C 391 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107884 restraints weight = 16985.097| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.94 r_work: 0.3081 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12123 Z= 0.196 Angle : 0.596 5.701 16521 Z= 0.317 Chirality : 0.041 0.151 1899 Planarity : 0.004 0.029 2016 Dihedral : 4.710 58.003 1629 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.81 % Allowed : 14.76 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1503 helix: -1.24 (0.13), residues: 1149 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.014 0.001 TYR A 146 PHE 0.028 0.002 PHE B 111 TRP 0.015 0.002 TRP B 96 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (12123) covalent geometry : angle 0.59641 / 0.32 (16521) hydrogen bonds : bond 0.05968 / 3.81 ( 711) hydrogen bonds : angle 4.36738 / 3.06 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.441 Fit side-chains REVERT: A 48 ASP cc_start: 0.8389 (t0) cc_final: 0.7914 (t0) REVERT: B 100 LEU cc_start: 0.8206 (tp) cc_final: 0.7924 (tp) REVERT: B 438 GLN cc_start: 0.7641 (tt0) cc_final: 0.7206 (tp40) outliers start: 47 outliers final: 22 residues processed: 224 average time/residue: 0.0917 time to fit residues: 31.5032 Evaluate side-chains 190 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS B 192 HIS B 443 ASN C 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102369 restraints weight = 16908.979| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.07 r_work: 0.3039 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12123 Z= 0.122 Angle : 0.489 6.095 16521 Z= 0.250 Chirality : 0.037 0.120 1899 Planarity : 0.003 0.026 2016 Dihedral : 4.134 55.192 1626 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 16.55 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1503 helix: -0.14 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -1.49 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 185 TYR 0.008 0.001 TYR A 146 PHE 0.023 0.001 PHE B 111 TRP 0.013 0.001 TRP A 365 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12123) covalent geometry : angle 0.48932 / 0.25 (16521) hydrogen bonds : bond 0.04824 / 3.06 ( 711) hydrogen bonds : angle 3.86129 / 2.71 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.417 Fit side-chains REVERT: A 48 ASP cc_start: 0.8262 (t0) cc_final: 0.7833 (t0) REVERT: B 100 LEU cc_start: 0.8299 (tp) cc_final: 0.8031 (tp) REVERT: B 438 GLN cc_start: 0.7814 (tt0) cc_final: 0.7356 (tp40) REVERT: B 493 MET cc_start: 0.8782 (ttm) cc_final: 0.8553 (mtp) REVERT: B 507 ARG cc_start: 0.6416 (ttp80) cc_final: 0.6094 (ttm170) REVERT: C 210 LEU cc_start: 0.8796 (tp) cc_final: 0.8164 (mm) outliers start: 28 outliers final: 19 residues processed: 199 average time/residue: 0.0974 time to fit residues: 29.5776 Evaluate side-chains 184 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 363 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN B 291 ASN B 371 ASN B 443 ASN C 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100733 restraints weight = 16777.789| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.02 r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12123 Z= 0.127 Angle : 0.483 5.919 16521 Z= 0.246 Chirality : 0.038 0.128 1899 Planarity : 0.003 0.026 2016 Dihedral : 4.075 52.980 1626 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.68 % Allowed : 16.71 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1503 helix: 0.31 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.33 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 185 TYR 0.009 0.001 TYR A 146 PHE 0.021 0.001 PHE B 111 TRP 0.011 0.001 TRP B 42 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12123) covalent geometry : angle 0.48255 / 0.25 (16521) hydrogen bonds : bond 0.04456 / 2.82 ( 711) hydrogen bonds : angle 3.69600 / 2.59 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.443 Fit side-chains REVERT: A 48 ASP cc_start: 0.8203 (t0) cc_final: 0.7769 (t0) REVERT: B 100 LEU cc_start: 0.8350 (tp) cc_final: 0.8110 (tp) REVERT: B 438 GLN cc_start: 0.7911 (tt0) cc_final: 0.7424 (tp40) REVERT: B 493 MET cc_start: 0.8756 (ttm) cc_final: 0.8530 (mtp) REVERT: B 507 ARG cc_start: 0.6430 (ttp80) cc_final: 0.6052 (ttm170) REVERT: C 210 LEU cc_start: 0.8771 (tp) cc_final: 0.8130 (mm) REVERT: C 465 MET cc_start: 0.8548 (tpp) cc_final: 0.8073 (mmt) outliers start: 33 outliers final: 25 residues processed: 198 average time/residue: 0.0905 time to fit residues: 27.4373 Evaluate side-chains 189 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 363 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.092628 restraints weight = 16765.573| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.28 r_work: 0.2878 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12123 Z= 0.129 Angle : 0.487 9.491 16521 Z= 0.245 Chirality : 0.038 0.123 1899 Planarity : 0.003 0.027 2016 Dihedral : 3.918 46.801 1626 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.33 % Allowed : 16.71 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1503 helix: 0.61 (0.16), residues: 1170 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 185 TYR 0.008 0.001 TYR A 146 PHE 0.018 0.001 PHE B 111 TRP 0.011 0.001 TRP B 42 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12123) covalent geometry : angle 0.48693 / 0.25 (16521) hydrogen bonds : bond 0.04374 / 2.77 ( 711) hydrogen bonds : angle 3.61541 / 2.55 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.431 Fit side-chains REVERT: A 48 ASP cc_start: 0.8111 (t0) cc_final: 0.7697 (t0) REVERT: A 263 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7161 (tt) REVERT: B 100 LEU cc_start: 0.8399 (tp) cc_final: 0.8179 (tp) REVERT: B 438 GLN cc_start: 0.7943 (tt0) cc_final: 0.7445 (tp40) REVERT: B 444 SER cc_start: 0.8165 (t) cc_final: 0.7930 (t) REVERT: B 493 MET cc_start: 0.8586 (ttm) cc_final: 0.8381 (mtp) REVERT: B 507 ARG cc_start: 0.6339 (ttp80) cc_final: 0.5916 (ttm170) REVERT: C 210 LEU cc_start: 0.8673 (tp) cc_final: 0.7969 (mm) REVERT: C 420 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6801 (t80) REVERT: C 465 MET cc_start: 0.8555 (tpp) cc_final: 0.8084 (mmt) outliers start: 41 outliers final: 31 residues processed: 197 average time/residue: 0.0823 time to fit residues: 24.8264 Evaluate side-chains 197 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093868 restraints weight = 16751.717| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.27 r_work: 0.2899 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12123 Z= 0.102 Angle : 0.461 8.200 16521 Z= 0.231 Chirality : 0.037 0.126 1899 Planarity : 0.002 0.026 2016 Dihedral : 3.841 46.806 1626 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.33 % Allowed : 16.95 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1503 helix: 0.89 (0.16), residues: 1167 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 185 TYR 0.007 0.001 TYR B 219 PHE 0.017 0.001 PHE B 111 TRP 0.011 0.001 TRP B 42 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (12123) covalent geometry : angle 0.46071 / 0.23 (16521) hydrogen bonds : bond 0.03884 / 2.45 ( 711) hydrogen bonds : angle 3.51592 / 2.48 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.404 Fit side-chains REVERT: A 48 ASP cc_start: 0.8078 (t0) cc_final: 0.7681 (t0) REVERT: A 74 CYS cc_start: 0.8023 (m) cc_final: 0.7603 (t) REVERT: A 263 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7184 (tt) REVERT: B 100 LEU cc_start: 0.8390 (tp) cc_final: 0.8174 (tp) REVERT: B 438 GLN cc_start: 0.7930 (tt0) cc_final: 0.7461 (tp40) REVERT: B 442 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 444 SER cc_start: 0.8121 (t) cc_final: 0.7833 (t) REVERT: B 507 ARG cc_start: 0.6411 (ttp80) cc_final: 0.5956 (ttm170) REVERT: C 210 LEU cc_start: 0.8659 (tp) cc_final: 0.7954 (mm) REVERT: C 419 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 465 MET cc_start: 0.8561 (tpp) cc_final: 0.8103 (mmt) outliers start: 41 outliers final: 30 residues processed: 196 average time/residue: 0.0883 time to fit residues: 26.6238 Evaluate side-chains 200 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 419 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 139 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 0.0020 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095156 restraints weight = 16631.707| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.28 r_work: 0.2913 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12123 Z= 0.090 Angle : 0.457 7.768 16521 Z= 0.225 Chirality : 0.036 0.127 1899 Planarity : 0.002 0.026 2016 Dihedral : 3.778 46.737 1626 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.76 % Allowed : 18.09 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1503 helix: 1.24 (0.16), residues: 1155 sheet: None (None), residues: 0 loop : -0.62 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 185 TYR 0.007 0.001 TYR B 219 PHE 0.015 0.001 PHE B 111 TRP 0.009 0.001 TRP B 42 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (12123) covalent geometry : angle 0.45734 / 0.22 (16521) hydrogen bonds : bond 0.03548 / 2.24 ( 711) hydrogen bonds : angle 3.44964 / 2.44 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.456 Fit side-chains REVERT: A 42 TRP cc_start: 0.8142 (m100) cc_final: 0.7841 (m100) REVERT: A 48 ASP cc_start: 0.8037 (t0) cc_final: 0.7658 (t0) REVERT: A 74 CYS cc_start: 0.7922 (m) cc_final: 0.7477 (t) REVERT: A 263 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7161 (tt) REVERT: B 100 LEU cc_start: 0.8393 (tp) cc_final: 0.8178 (tp) REVERT: B 438 GLN cc_start: 0.7926 (tt0) cc_final: 0.7445 (tp40) REVERT: B 442 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 444 SER cc_start: 0.8097 (t) cc_final: 0.7854 (m) REVERT: B 507 ARG cc_start: 0.6382 (ttp80) cc_final: 0.5920 (ttm170) REVERT: C 210 LEU cc_start: 0.8626 (tp) cc_final: 0.7937 (mm) REVERT: C 419 LEU cc_start: 0.8568 (tp) cc_final: 0.8213 (mp) REVERT: C 420 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.6770 (t80) REVERT: C 465 MET cc_start: 0.8536 (tpp) cc_final: 0.8090 (mmt) outliers start: 34 outliers final: 25 residues processed: 196 average time/residue: 0.1041 time to fit residues: 31.2294 Evaluate side-chains 191 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 420 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092519 restraints weight = 16806.194| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.28 r_work: 0.2874 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12123 Z= 0.131 Angle : 0.492 6.951 16521 Z= 0.245 Chirality : 0.038 0.124 1899 Planarity : 0.003 0.026 2016 Dihedral : 3.797 46.490 1626 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.33 % Allowed : 17.68 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1503 helix: 1.08 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.02 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 185 TYR 0.009 0.001 TYR A 146 PHE 0.016 0.001 PHE B 111 TRP 0.010 0.001 TRP B 42 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (12123) covalent geometry : angle 0.49154 / 0.25 (16521) hydrogen bonds : bond 0.04212 / 2.67 ( 711) hydrogen bonds : angle 3.49104 / 2.47 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.455 Fit side-chains REVERT: A 48 ASP cc_start: 0.8023 (t0) cc_final: 0.7640 (t0) REVERT: A 263 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 100 LEU cc_start: 0.8388 (tp) cc_final: 0.8139 (tp) REVERT: B 444 SER cc_start: 0.8201 (t) cc_final: 0.7997 (m) REVERT: B 507 ARG cc_start: 0.6423 (ttp80) cc_final: 0.5878 (ttm170) REVERT: C 210 LEU cc_start: 0.8660 (tp) cc_final: 0.7932 (mm) REVERT: C 419 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 420 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6957 (t80) REVERT: C 465 MET cc_start: 0.8568 (tpp) cc_final: 0.8104 (mmt) outliers start: 41 outliers final: 33 residues processed: 195 average time/residue: 0.0964 time to fit residues: 28.4950 Evaluate side-chains 199 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 420 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 93 optimal weight: 0.0050 chunk 7 optimal weight: 0.0000 chunk 28 optimal weight: 0.6980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN A 192 HIS B 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095402 restraints weight = 16548.586| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.27 r_work: 0.2920 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12123 Z= 0.087 Angle : 0.460 7.289 16521 Z= 0.225 Chirality : 0.036 0.128 1899 Planarity : 0.002 0.025 2016 Dihedral : 3.689 46.253 1626 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.11 % Allowed : 18.82 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.23), residues: 1503 helix: 1.49 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 185 TYR 0.006 0.001 TYR B 219 PHE 0.015 0.001 PHE B 111 TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (12123) covalent geometry : angle 0.45987 / 0.23 (16521) hydrogen bonds : bond 0.03387 / 2.13 ( 711) hydrogen bonds : angle 3.39291 / 2.41 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.380 Fit side-chains REVERT: A 48 ASP cc_start: 0.7943 (t0) cc_final: 0.7541 (t0) REVERT: A 263 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7153 (tt) REVERT: B 31 THR cc_start: 0.8629 (m) cc_final: 0.8422 (m) REVERT: B 100 LEU cc_start: 0.8335 (tp) cc_final: 0.8087 (tp) REVERT: B 507 ARG cc_start: 0.6384 (ttp80) cc_final: 0.5834 (ttm170) REVERT: C 210 LEU cc_start: 0.8600 (tp) cc_final: 0.7917 (mm) REVERT: C 419 LEU cc_start: 0.8528 (tp) cc_final: 0.8166 (mp) REVERT: C 465 MET cc_start: 0.8537 (tpp) cc_final: 0.8097 (mmt) outliers start: 26 outliers final: 21 residues processed: 187 average time/residue: 0.0889 time to fit residues: 24.9816 Evaluate side-chains 188 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 124 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.093572 restraints weight = 16770.213| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.27 r_work: 0.2890 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12123 Z= 0.114 Angle : 0.488 9.773 16521 Z= 0.239 Chirality : 0.038 0.158 1899 Planarity : 0.002 0.027 2016 Dihedral : 3.670 46.356 1626 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.11 % Allowed : 18.82 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.23), residues: 1503 helix: 1.47 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 340 TYR 0.007 0.001 TYR A 146 PHE 0.024 0.001 PHE B 38 TRP 0.010 0.001 TRP B 42 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (12123) covalent geometry : angle 0.48838 / 0.24 (16521) hydrogen bonds : bond 0.03854 / 2.44 ( 711) hydrogen bonds : angle 3.40161 / 2.41 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.494 Fit side-chains REVERT: A 48 ASP cc_start: 0.7962 (t0) cc_final: 0.7591 (t0) REVERT: B 31 THR cc_start: 0.8612 (m) cc_final: 0.8388 (m) REVERT: B 100 LEU cc_start: 0.8341 (tp) cc_final: 0.8094 (tp) REVERT: B 507 ARG cc_start: 0.6462 (ttp80) cc_final: 0.5876 (ttm170) REVERT: C 210 LEU cc_start: 0.8632 (tp) cc_final: 0.7932 (mm) REVERT: C 419 LEU cc_start: 0.8589 (tp) cc_final: 0.8199 (mp) REVERT: C 420 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6979 (t80) REVERT: C 465 MET cc_start: 0.8568 (tpp) cc_final: 0.8115 (mmt) outliers start: 26 outliers final: 22 residues processed: 184 average time/residue: 0.0943 time to fit residues: 26.4686 Evaluate side-chains 189 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093714 restraints weight = 16748.562| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.28 r_work: 0.2893 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12123 Z= 0.109 Angle : 0.487 9.398 16521 Z= 0.238 Chirality : 0.038 0.201 1899 Planarity : 0.002 0.027 2016 Dihedral : 3.690 46.373 1626 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.27 % Allowed : 18.49 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1503 helix: 1.54 (0.16), residues: 1146 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 340 TYR 0.007 0.001 TYR B 121 PHE 0.023 0.001 PHE B 38 TRP 0.010 0.001 TRP B 42 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12123) covalent geometry : angle 0.48694 / 0.24 (16521) hydrogen bonds : bond 0.03796 / 2.40 ( 711) hydrogen bonds : angle 3.40123 / 2.41 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3338.70 seconds wall clock time: 57 minutes 50.16 seconds (3470.16 seconds total)