Starting phenix.real_space_refine on Fri Jul 3 17:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm1_32597/07_2026/7wm1_32597.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.144 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 72 5.16 5 C 9948 2.51 5 N 2516 2.21 5 O 2654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15197 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "B" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "C" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "D" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 3.52, per 1000 atoms: 0.23 Number of scatterers: 15197 At special positions: 0 Unit cell: (115.271, 113.117, 123.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 72 16.00 P 4 15.00 O 2654 8.00 N 2516 7.00 C 9948 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: 1.14 Conformation dependent library (CDL) restraints added in 664.8 milliseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 12 sheets defined 58.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.575A pdb=" N TRP A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 107 removed outlier: 3.575A pdb=" N ILE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 4.361A pdb=" N PHE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.717A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.795A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 215 removed outlier: 4.111A pdb=" N ALA A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.599A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 290 removed outlier: 3.642A pdb=" N MET A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.603A pdb=" N ARG A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.763A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.798A pdb=" N GLU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.609A pdb=" N LEU A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 369 removed outlier: 3.585A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.662A pdb=" N GLU A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 467 through 476 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 83 through 110 removed outlier: 3.835A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.633A pdb=" N VAL B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 163 through 173 removed outlier: 4.218A pdb=" N VAL B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU B 199 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 203 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.635A pdb=" N LYS B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.547A pdb=" N ARG B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 288 removed outlier: 3.604A pdb=" N GLY B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 277 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.800A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 352 removed outlier: 3.765A pdb=" N SER B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 removed outlier: 3.686A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.632A pdb=" N HIS B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.955A pdb=" N ILE B 401 " --> pdb=" O PHE B 397 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 474 through 481 removed outlier: 4.015A pdb=" N VAL B 478 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 518 through 526 Processing helix chain 'C' and resid 54 through 81 removed outlier: 3.515A pdb=" N ALA C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 107 removed outlier: 3.574A pdb=" N ILE C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 132 removed outlier: 4.306A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.717A pdb=" N ARG C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.795A pdb=" N GLY C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 192 through 215 removed outlier: 3.682A pdb=" N CYS C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 253 removed outlier: 3.599A pdb=" N TYR C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 290 removed outlier: 3.641A pdb=" N MET C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.604A pdb=" N ARG C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.763A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.736A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.609A pdb=" N LEU C 350 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 369 removed outlier: 3.585A pdb=" N SER C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.661A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 467 through 476 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 83 through 110 removed outlier: 3.835A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.634A pdb=" N VAL D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 163 through 173 removed outlier: 4.217A pdb=" N VAL D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU D 199 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 203 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.634A pdb=" N LYS D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 251 removed outlier: 3.535A pdb=" N LEU D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 288 removed outlier: 3.603A pdb=" N GLY D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 277 " --> pdb=" O TRP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.801A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 4.076A pdb=" N ASP D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 376 removed outlier: 3.685A pdb=" N ARG D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 removed outlier: 3.633A pdb=" N HIS D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.956A pdb=" N ILE D 401 " --> pdb=" O PHE D 397 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 403 " --> pdb=" O SER D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 474 through 481 removed outlier: 4.015A pdb=" N VAL D 478 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 518 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.755A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 433 removed outlier: 3.872A pdb=" N SER A 428 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 421 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'B' and resid 424 through 427 removed outlier: 7.040A pdb=" N GLN B 495 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 432 through 434 removed outlier: 6.789A pdb=" N VAL B 488 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 451 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS B 466 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 453 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 462 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.755A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 428 through 429 removed outlier: 3.872A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'D' and resid 424 through 427 removed outlier: 7.040A pdb=" N GLN D 495 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 432 through 434 removed outlier: 6.787A pdb=" N VAL D 488 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 451 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS D 466 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 453 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 462 " --> pdb=" O ALA D 455 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2064 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: 2.46 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 26 1.15 - 1.31: 2358 1.31 - 1.48: 6419 1.48 - 1.65: 6637 1.65 - 1.81: 126 Bond restraints: 15566 Sorted by residual: bond pdb=" C TRP C 73 " pdb=" O TRP C 73 " ideal model delta sigma weight residual 1.236 0.982 0.254 1.15e-02 7.56e+03 4.89e+02 bond pdb=" C ALA C 72 " pdb=" O ALA C 72 " ideal model delta sigma weight residual 1.237 0.982 0.255 1.16e-02 7.43e+03 4.83e+02 bond pdb=" C THR C 71 " pdb=" O THR C 71 " ideal model delta sigma weight residual 1.236 1.010 0.226 1.28e-02 6.10e+03 3.11e+02 bond pdb=" C PRO C 76 " pdb=" O PRO C 76 " ideal model delta sigma weight residual 1.237 1.041 0.196 1.26e-02 6.30e+03 2.42e+02 bond pdb=" C PHE C 77 " pdb=" O PHE C 77 " ideal model delta sigma weight residual 1.236 1.044 0.192 1.26e-02 6.30e+03 2.33e+02 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 20847 4.63 - 9.25: 205 9.25 - 13.88: 22 13.88 - 18.51: 9 18.51 - 23.14: 3 Bond angle restraints: 21086 Sorted by residual: angle pdb=" C LEU D 60 " pdb=" N PRO D 61 " pdb=" CA PRO D 61 " ideal model delta sigma weight residual 119.90 135.40 -15.50 1.05e+00 9.07e-01 2.18e+02 angle pdb=" C TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta sigma weight residual 110.88 87.74 23.14 1.57e+00 4.06e-01 2.17e+02 angle pdb=" C TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta sigma weight residual 110.88 87.77 23.11 1.57e+00 4.06e-01 2.17e+02 angle pdb=" O MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 122.39 101.53 20.86 1.48e+00 4.57e-01 1.99e+02 angle pdb=" CA MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 118.44 135.44 -17.00 1.41e+00 5.03e-01 1.45e+02 ... (remaining 21081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 8266 26.62 - 53.25: 792 53.25 - 79.87: 130 79.87 - 106.49: 16 106.49 - 133.11: 2 Dihedral angle restraints: 9206 sinusoidal: 3770 harmonic: 5436 Sorted by residual: dihedral pdb=" C TYR A 57 " pdb=" N TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta harmonic sigma weight residual -122.60 -95.90 -26.70 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C TYR C 57 " pdb=" N TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta harmonic sigma weight residual -122.60 -95.92 -26.68 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C ASP C 54 " pdb=" N ASP C 54 " pdb=" CA ASP C 54 " pdb=" CB ASP C 54 " ideal model delta harmonic sigma weight residual -122.60 -144.47 21.87 0 2.50e+00 1.60e-01 7.65e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2275 0.170 - 0.340: 71 0.340 - 0.510: 19 0.510 - 0.680: 2 0.680 - 0.851: 3 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA PRO C 76 " pdb=" N PRO C 76 " pdb=" C PRO C 76 " pdb=" CB PRO C 76 " both_signs ideal model delta sigma weight residual False 2.72 1.87 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA ASP C 54 " pdb=" N ASP C 54 " pdb=" C ASP C 54 " pdb=" CB ASP C 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA ASP A 54 " pdb=" N ASP A 54 " pdb=" C ASP A 54 " pdb=" CB ASP A 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 ... (remaining 2367 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 701 " -0.252 2.00e-02 2.50e+03 2.37e-01 5.63e+02 pdb=" C29 POV B 701 " 0.308 2.00e-02 2.50e+03 pdb="C210 POV B 701 " 0.153 2.00e-02 2.50e+03 pdb="C211 POV B 701 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 901 " 0.141 2.00e-02 2.50e+03 1.41e-01 1.99e+02 pdb=" C29 POV C 901 " -0.139 2.00e-02 2.50e+03 pdb="C210 POV C 901 " -0.143 2.00e-02 2.50e+03 pdb="C211 POV C 901 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " 0.119 2.00e-02 2.50e+03 1.18e-01 1.39e+02 pdb=" C29 POV D 701 " -0.127 2.00e-02 2.50e+03 pdb="C210 POV D 701 " -0.109 2.00e-02 2.50e+03 pdb="C211 POV D 701 " 0.116 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 663 2.69 - 3.30: 17049 3.30 - 3.92: 27668 3.92 - 4.53: 39251 4.53 - 5.14: 61322 Nonbonded interactions: 145953 Sorted by model distance: nonbonded pdb=" N ASP D 344 " pdb=" OD1 ASP D 344 " model vdw 2.080 3.120 nonbonded pdb=" O THR D 288 " pdb=" OG1 THR D 289 " model vdw 2.144 3.040 nonbonded pdb=" O THR B 288 " pdb=" OG1 THR B 289 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" O22 POV A 901 " model vdw 2.200 3.040 nonbonded pdb=" N ASP B 452 " pdb=" OD1 ASP B 452 " model vdw 2.206 3.120 ... (remaining 145948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 901) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.320 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.310 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.012 0.255 15566 Z= 0.781 Angle : 1.248 23.135 21086 Z= 0.816 Chirality : 0.082 0.851 2370 Planarity : 0.010 0.237 2622 Dihedral : 20.137 133.112 5694 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 15.89 % Allowed : 23.78 % Favored : 60.33 % Cbeta Deviations : 1.94 % 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: -4.36 (0.16), residues: 1836 helix: -2.85 (0.12), residues: 1044 sheet: -1.83 (0.46), residues: 100 loop : -2.87 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 226 TYR 0.039 0.003 TYR C 70 PHE 0.061 0.003 PHE B 63 TRP 0.083 0.005 TRP C 73 HIS 0.009 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.01189 / 0.78 (15566) covalent geometry : angle 1.24805 / 0.82 (21086) hydrogen bonds : bond 0.23151 / 14.83 ( 718) hydrogen bonds : angle 8.20439 / 5.73 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 294 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.3386 (OUTLIER) cc_final: 0.2971 (mtmm) REVERT: A 47 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4459 (ptt180) REVERT: A 54 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7318 (p0) REVERT: A 55 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7224 (m170) REVERT: A 233 GLU cc_start: 0.7125 (pm20) cc_final: 0.6911 (pp20) REVERT: A 322 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 356 SER cc_start: 0.8771 (p) cc_final: 0.8438 (m) REVERT: A 368 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7285 (t70) REVERT: A 429 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6730 (tt) REVERT: B 319 TYR cc_start: 0.7854 (t80) cc_final: 0.7499 (t80) REVERT: B 324 MET cc_start: 0.8008 (tpp) cc_final: 0.7705 (tpt) REVERT: B 394 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (tm130) REVERT: B 418 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 519 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6379 (pp) REVERT: B 520 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7217 (mm) REVERT: C 44 LYS cc_start: 0.3295 (OUTLIER) cc_final: 0.2990 (mtmt) REVERT: C 47 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4660 (ptt180) REVERT: C 55 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7135 (m170) REVERT: C 151 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7030 (mmt90) REVERT: C 188 TRP cc_start: 0.8076 (m100) cc_final: 0.7737 (m100) REVERT: C 322 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 342 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7637 (mm-40) REVERT: C 368 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6975 (p0) REVERT: C 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 392 TYR cc_start: 0.7968 (m-80) cc_final: 0.7707 (m-80) REVERT: C 429 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6756 (tt) REVERT: C 448 ARG cc_start: 0.7319 (ptp-110) cc_final: 0.7068 (ptp90) REVERT: D 167 VAL cc_start: 0.8407 (p) cc_final: 0.8195 (m) REVERT: D 280 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: D 319 TYR cc_start: 0.7779 (t80) cc_final: 0.7447 (t80) REVERT: D 324 MET cc_start: 0.7990 (tpp) cc_final: 0.7710 (tpt) REVERT: D 336 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5208 (t80) REVERT: D 338 MET cc_start: 0.6954 (tpp) cc_final: 0.6640 (ttm) REVERT: D 359 ARG cc_start: 0.6590 (ttm110) cc_final: 0.6229 (ttm110) REVERT: D 520 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7386 (mm) outliers start: 260 outliers final: 89 residues processed: 504 average time/residue: 0.5101 time to fit residues: 287.0406 Evaluate side-chains 328 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 218 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 218 ASN A 323 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 461 GLN A 487 ASN A 491 HIS B 219 HIS B 299 ASN B 330 HIS B 436 GLN B 501 HIS B 502 HIS B 522 ASN C 97 ASN C 218 ASN C 323 GLN C 342 GLN C 378 ASN C 461 GLN C 487 ASN C 491 HIS D 219 HIS D 299 ASN D 436 GLN D 501 HIS D 502 HIS D 509 GLN D 522 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.208377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140716 restraints weight = 16452.815| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.15 r_work: 0.3356 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15566 Z= 0.135 Angle : 0.623 8.468 21086 Z= 0.330 Chirality : 0.044 0.179 2370 Planarity : 0.005 0.043 2622 Dihedral : 13.163 112.183 2360 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 7.70 % Allowed : 28.85 % Favored : 63.45 % 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: -2.60 (0.18), residues: 1836 helix: -1.37 (0.15), residues: 1050 sheet: -1.52 (0.41), residues: 122 loop : -2.14 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.022 0.002 TYR A 334 PHE 0.020 0.002 PHE B 486 TRP 0.014 0.002 TRP A 60 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15566) covalent geometry : angle 0.62323 / 0.33 (21086) hydrogen bonds : bond 0.04847 / 3.20 ( 718) hydrogen bonds : angle 4.57158 / 3.20 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 250 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5320 (mmt-90) REVERT: A 47 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4540 (ptt90) REVERT: A 51 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.7370 (t) REVERT: A 55 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.5999 (m170) REVERT: A 151 ARG cc_start: 0.7116 (tpp80) cc_final: 0.5552 (mtm180) REVERT: A 155 GLN cc_start: 0.6730 (mm-40) cc_final: 0.6304 (tp-100) REVERT: A 168 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 233 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7334 (pp20) REVERT: A 321 ARG cc_start: 0.7340 (mmm160) cc_final: 0.7070 (mmm160) REVERT: A 343 GLN cc_start: 0.5717 (OUTLIER) cc_final: 0.5426 (tp40) REVERT: A 465 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7664 (tpt) REVERT: B 168 MET cc_start: 0.7321 (mmt) cc_final: 0.7015 (mmm) REVERT: B 209 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6222 (pt0) REVERT: B 319 TYR cc_start: 0.8021 (t80) cc_final: 0.7703 (t80) REVERT: B 394 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7652 (tm130) REVERT: B 403 GLU cc_start: 0.6526 (pt0) cc_final: 0.5961 (pp20) REVERT: B 418 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6197 (mt) REVERT: B 484 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6715 (tp-100) REVERT: B 519 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6115 (pp) REVERT: C 47 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.4663 (ptt180) REVERT: C 151 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6742 (mmt90) REVERT: C 188 TRP cc_start: 0.7687 (m100) cc_final: 0.7444 (m100) REVERT: C 233 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: C 321 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7262 (mmm160) REVERT: C 367 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6905 (tpp) REVERT: C 392 TYR cc_start: 0.7967 (m-80) cc_final: 0.7666 (m-80) REVERT: C 429 ILE cc_start: 0.7242 (mp) cc_final: 0.7006 (tt) REVERT: C 431 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7484 (ptm-80) REVERT: C 448 ARG cc_start: 0.7711 (ptp-110) cc_final: 0.7451 (ptp90) REVERT: C 465 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7458 (tpt) REVERT: D 168 MET cc_start: 0.7314 (mmt) cc_final: 0.6969 (mmm) REVERT: D 209 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6123 (pt0) REVERT: D 280 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8701 (mmp) REVERT: D 319 TYR cc_start: 0.8096 (t80) cc_final: 0.7510 (t80) REVERT: D 338 MET cc_start: 0.5944 (tpp) cc_final: 0.5714 (tpt) REVERT: D 367 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6672 (mm110) REVERT: D 394 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: D 403 GLU cc_start: 0.6403 (pt0) cc_final: 0.5933 (pp20) REVERT: D 418 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6112 (mt) REVERT: D 432 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7391 (pt0) REVERT: D 484 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6427 (tp-100) REVERT: D 519 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6159 (pp) outliers start: 126 outliers final: 38 residues processed: 350 average time/residue: 0.5662 time to fit residues: 219.6324 Evaluate side-chains 275 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 352 ASN C 487 ASN D 219 HIS D 352 ASN D 522 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.208485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142784 restraints weight = 16527.379| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.13 r_work: 0.3338 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15566 Z= 0.143 Angle : 0.577 8.727 21086 Z= 0.304 Chirality : 0.043 0.158 2370 Planarity : 0.004 0.042 2622 Dihedral : 10.910 95.142 2235 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 7.09 % Allowed : 29.77 % Favored : 63.14 % 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: -1.72 (0.19), residues: 1836 helix: -0.63 (0.16), residues: 1056 sheet: -1.07 (0.44), residues: 116 loop : -1.82 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.019 0.002 TYR D 405 PHE 0.020 0.001 PHE B 110 TRP 0.013 0.002 TRP D 273 HIS 0.008 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15566) covalent geometry : angle 0.57719 / 0.30 (21086) hydrogen bonds : bond 0.04599 / 3.03 ( 718) hydrogen bonds : angle 4.13268 / 2.90 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 237 time to evaluate : 0.605 Fit side-chains REVERT: A 47 ARG cc_start: 0.5130 (OUTLIER) cc_final: 0.4372 (ptt90) REVERT: A 55 HIS cc_start: 0.6547 (OUTLIER) cc_final: 0.6185 (m170) REVERT: A 151 ARG cc_start: 0.7004 (tpp80) cc_final: 0.5488 (mtm180) REVERT: A 155 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6657 (tp-100) REVERT: A 168 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 182 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5992 (mpp80) REVERT: A 233 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: A 331 CYS cc_start: 0.7864 (m) cc_final: 0.7108 (p) REVERT: A 431 ARG cc_start: 0.8167 (ptm-80) cc_final: 0.7898 (ptm-80) REVERT: B 66 PHE cc_start: 0.7726 (t80) cc_final: 0.7506 (t80) REVERT: B 197 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8284 (p0) REVERT: B 209 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6551 (pt0) REVERT: B 257 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7954 (t70) REVERT: B 319 TYR cc_start: 0.8243 (t80) cc_final: 0.7970 (t80) REVERT: B 339 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6062 (ttm110) REVERT: B 360 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: B 394 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: B 403 GLU cc_start: 0.6764 (pt0) cc_final: 0.6082 (pm20) REVERT: B 418 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6431 (mt) REVERT: B 423 GLN cc_start: 0.6571 (pm20) cc_final: 0.6340 (pm20) REVERT: B 466 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6769 (mptt) REVERT: B 484 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6613 (mm-40) REVERT: B 512 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6639 (t0) REVERT: B 519 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6236 (pp) REVERT: C 47 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4504 (ptt90) REVERT: C 151 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6722 (mmt90) REVERT: C 155 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6498 (tp-100) REVERT: C 182 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.6131 (mpp80) REVERT: C 188 TRP cc_start: 0.7719 (m100) cc_final: 0.7453 (m100) REVERT: C 233 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: C 331 CYS cc_start: 0.7872 (m) cc_final: 0.6997 (p) REVERT: C 392 TYR cc_start: 0.8141 (m-80) cc_final: 0.7831 (m-80) REVERT: C 429 ILE cc_start: 0.7333 (mp) cc_final: 0.7112 (tt) REVERT: D 197 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (p0) REVERT: D 209 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6409 (pt0) REVERT: D 257 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7941 (t70) REVERT: D 280 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8781 (mmp) REVERT: D 319 TYR cc_start: 0.8238 (t80) cc_final: 0.7795 (t80) REVERT: D 334 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5743 (mmp-170) REVERT: D 394 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: D 403 GLU cc_start: 0.6809 (pt0) cc_final: 0.6066 (pm20) REVERT: D 432 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7311 (pt0) REVERT: D 484 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6656 (tp-100) REVERT: D 512 ASN cc_start: 0.6763 (m-40) cc_final: 0.6476 (t0) REVERT: D 519 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6223 (pp) outliers start: 116 outliers final: 42 residues processed: 324 average time/residue: 0.5745 time to fit residues: 205.7243 Evaluate side-chains 287 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 512 ASN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN A 486 ASN B 219 HIS C 342 GLN C 487 ASN D 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137054 restraints weight = 16437.200| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.08 r_work: 0.3300 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15566 Z= 0.213 Angle : 0.631 7.978 21086 Z= 0.334 Chirality : 0.046 0.164 2370 Planarity : 0.004 0.046 2622 Dihedral : 10.590 85.773 2217 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 7.70 % Allowed : 30.38 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 1836 helix: -0.47 (0.16), residues: 1082 sheet: -0.63 (0.46), residues: 106 loop : -1.84 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.015 0.002 TYR A 283 PHE 0.028 0.002 PHE D 110 TRP 0.014 0.002 TRP D 273 HIS 0.008 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (15566) covalent geometry : angle 0.63083 / 0.33 (21086) hydrogen bonds : bond 0.05119 / 3.36 ( 718) hydrogen bonds : angle 4.18202 / 2.93 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 231 time to evaluate : 0.634 Fit side-chains REVERT: A 47 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.4477 (ptt90) REVERT: A 55 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.6216 (m170) REVERT: A 106 MET cc_start: 0.6410 (ttp) cc_final: 0.6194 (tmm) REVERT: A 151 ARG cc_start: 0.6938 (tpp80) cc_final: 0.5340 (mtm180) REVERT: A 168 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7447 (mp) REVERT: A 182 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.6001 (mpp80) REVERT: A 233 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6943 (pp20) REVERT: A 321 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7117 (mmm160) REVERT: A 331 CYS cc_start: 0.7758 (m) cc_final: 0.6952 (p) REVERT: A 335 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6145 (mpt-90) REVERT: A 388 MET cc_start: 0.8149 (ttt) cc_final: 0.7927 (ttp) REVERT: A 431 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7826 (ptm-80) REVERT: B 66 PHE cc_start: 0.7732 (t80) cc_final: 0.7529 (t80) REVERT: B 140 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 197 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 209 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6178 (pt0) REVERT: B 257 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7927 (t70) REVERT: B 319 TYR cc_start: 0.8068 (t80) cc_final: 0.7861 (t80) REVERT: B 339 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6084 (ttm110) REVERT: B 360 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: B 394 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: B 403 GLU cc_start: 0.6662 (pt0) cc_final: 0.5898 (pm20) REVERT: B 418 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6141 (mt) REVERT: B 423 GLN cc_start: 0.6435 (pm20) cc_final: 0.6153 (pm20) REVERT: B 484 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mm110) REVERT: B 519 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6182 (pp) REVERT: C 47 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.4451 (ptt90) REVERT: C 106 MET cc_start: 0.6236 (ttp) cc_final: 0.6022 (tmm) REVERT: C 151 ARG cc_start: 0.7033 (tpp80) cc_final: 0.5496 (mtm180) REVERT: C 155 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6582 (tp-100) REVERT: C 168 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7444 (mp) REVERT: C 182 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.6001 (mpp80) REVERT: C 188 TRP cc_start: 0.7746 (m100) cc_final: 0.7521 (m100) REVERT: C 233 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: C 331 CYS cc_start: 0.7755 (m) cc_final: 0.7013 (p) REVERT: C 387 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: C 392 TYR cc_start: 0.8051 (m-80) cc_final: 0.7749 (m-80) REVERT: D 140 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7711 (p) REVERT: D 197 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8067 (p0) REVERT: D 209 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6182 (pt0) REVERT: D 257 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7905 (t70) REVERT: D 280 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8788 (mmp) REVERT: D 319 TYR cc_start: 0.8075 (t80) cc_final: 0.7736 (t80) REVERT: D 334 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5618 (mmp-170) REVERT: D 362 MET cc_start: 0.7648 (mtp) cc_final: 0.7380 (mtm) REVERT: D 394 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 403 GLU cc_start: 0.6659 (pt0) cc_final: 0.5906 (pm20) REVERT: D 484 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6449 (tp-100) REVERT: D 519 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6188 (pp) outliers start: 126 outliers final: 51 residues processed: 330 average time/residue: 0.5171 time to fit residues: 189.6950 Evaluate side-chains 291 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 212 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN B 219 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 221 ASN D 330 HIS D 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.210147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141309 restraints weight = 16525.397| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.92 r_work: 0.3357 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15566 Z= 0.124 Angle : 0.547 8.724 21086 Z= 0.287 Chirality : 0.042 0.146 2370 Planarity : 0.004 0.041 2622 Dihedral : 9.793 82.565 2215 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 7.09 % Allowed : 31.23 % Favored : 61.67 % 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: -1.04 (0.20), residues: 1836 helix: 0.01 (0.16), residues: 1070 sheet: -0.78 (0.45), residues: 116 loop : -1.76 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.020 0.001 TYR B 405 PHE 0.018 0.001 PHE B 110 TRP 0.009 0.001 TRP B 273 HIS 0.008 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15566) covalent geometry : angle 0.54712 / 0.29 (21086) hydrogen bonds : bond 0.04100 / 2.71 ( 718) hydrogen bonds : angle 3.85266 / 2.70 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 238 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.4414 (ptt90) REVERT: A 55 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.6201 (m170) REVERT: A 151 ARG cc_start: 0.6811 (tpp80) cc_final: 0.5262 (mtm180) REVERT: A 162 MET cc_start: 0.8537 (tpt) cc_final: 0.8088 (mmm) REVERT: A 182 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.6047 (mpp80) REVERT: A 233 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: A 321 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7151 (mmm160) REVERT: A 331 CYS cc_start: 0.7639 (m) cc_final: 0.6995 (p) REVERT: A 335 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6107 (mpt-90) REVERT: B 66 PHE cc_start: 0.7621 (t80) cc_final: 0.7364 (t80) REVERT: B 209 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6244 (pt0) REVERT: B 257 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7885 (t70) REVERT: B 339 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5935 (ttm110) REVERT: B 360 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: B 394 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 403 GLU cc_start: 0.6676 (pt0) cc_final: 0.6073 (pm20) REVERT: B 418 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6086 (mt) REVERT: B 423 GLN cc_start: 0.6077 (pm20) cc_final: 0.5657 (pm20) REVERT: B 484 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6305 (mm-40) REVERT: B 519 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.6127 (pp) REVERT: C 47 ARG cc_start: 0.5127 (OUTLIER) cc_final: 0.4434 (ptt90) REVERT: C 106 MET cc_start: 0.5966 (ttp) cc_final: 0.5744 (tmm) REVERT: C 151 ARG cc_start: 0.6887 (tpp80) cc_final: 0.5366 (mtm180) REVERT: C 162 MET cc_start: 0.8481 (tpt) cc_final: 0.8032 (mmm) REVERT: C 182 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5994 (mpp80) REVERT: C 188 TRP cc_start: 0.7494 (m100) cc_final: 0.7278 (m100) REVERT: C 233 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: C 331 CYS cc_start: 0.7622 (m) cc_final: 0.6927 (p) REVERT: C 387 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: C 392 TYR cc_start: 0.7925 (m-80) cc_final: 0.7600 (m-80) REVERT: D 66 PHE cc_start: 0.7787 (t80) cc_final: 0.7562 (t80) REVERT: D 209 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6222 (pt0) REVERT: D 257 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7954 (t70) REVERT: D 280 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8646 (mmp) REVERT: D 319 TYR cc_start: 0.8026 (t80) cc_final: 0.7632 (t80) REVERT: D 362 MET cc_start: 0.7429 (mtp) cc_final: 0.7183 (mtm) REVERT: D 376 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: D 394 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: D 403 GLU cc_start: 0.6796 (pt0) cc_final: 0.6189 (pm20) REVERT: D 421 GLN cc_start: 0.7650 (mp10) cc_final: 0.7149 (mp10) REVERT: D 432 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6206 (pt0) REVERT: D 484 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.6333 (tp-100) REVERT: D 519 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6244 (pp) outliers start: 116 outliers final: 47 residues processed: 325 average time/residue: 0.5514 time to fit residues: 198.4211 Evaluate side-chains 282 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 152 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN B 219 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.209369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143477 restraints weight = 16387.609| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.12 r_work: 0.3334 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15566 Z= 0.136 Angle : 0.556 7.902 21086 Z= 0.291 Chirality : 0.043 0.155 2370 Planarity : 0.004 0.039 2622 Dihedral : 9.612 83.088 2207 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 6.60 % Allowed : 32.03 % Favored : 61.37 % 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: -0.89 (0.19), residues: 1836 helix: 0.17 (0.16), residues: 1072 sheet: -0.81 (0.45), residues: 116 loop : -1.75 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.011 0.001 TYR B 405 PHE 0.020 0.001 PHE B 110 TRP 0.010 0.002 TRP D 273 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15566) covalent geometry : angle 0.55631 / 0.29 (21086) hydrogen bonds : bond 0.04232 / 2.80 ( 718) hydrogen bonds : angle 3.82074 / 2.69 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 223 time to evaluate : 0.380 Fit side-chains REVERT: A 47 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4401 (ptt90) REVERT: A 55 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6372 (m170) REVERT: A 151 ARG cc_start: 0.6905 (tpp80) cc_final: 0.5409 (mtm180) REVERT: A 152 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 162 MET cc_start: 0.8753 (tpt) cc_final: 0.8302 (mmm) REVERT: A 182 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5995 (mpp80) REVERT: A 233 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: A 321 ARG cc_start: 0.7489 (mmm160) cc_final: 0.7159 (mmm160) REVERT: A 331 CYS cc_start: 0.7982 (m) cc_final: 0.7319 (p) REVERT: A 335 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6160 (mpt-90) REVERT: B 66 PHE cc_start: 0.7669 (t80) cc_final: 0.7421 (t80) REVERT: B 168 MET cc_start: 0.7525 (mmt) cc_final: 0.7219 (mmm) REVERT: B 197 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8238 (p0) REVERT: B 209 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6722 (pt0) REVERT: B 257 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (t70) REVERT: B 360 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: B 362 MET cc_start: 0.7773 (mtp) cc_final: 0.7499 (mtm) REVERT: B 375 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7210 (pt) REVERT: B 394 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 403 GLU cc_start: 0.7123 (pt0) cc_final: 0.6531 (pm20) REVERT: B 423 GLN cc_start: 0.6172 (pm20) cc_final: 0.5835 (pm20) REVERT: B 432 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6546 (pt0) REVERT: B 435 LEU cc_start: 0.8013 (mt) cc_final: 0.7775 (mm) REVERT: B 484 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6575 (mm110) REVERT: B 519 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6242 (pp) REVERT: C 47 ARG cc_start: 0.5131 (OUTLIER) cc_final: 0.4454 (ptt90) REVERT: C 106 MET cc_start: 0.6489 (ttp) cc_final: 0.6227 (tmm) REVERT: C 151 ARG cc_start: 0.6938 (tpp80) cc_final: 0.5461 (mtm180) REVERT: C 162 MET cc_start: 0.8732 (tpt) cc_final: 0.8300 (mmm) REVERT: C 188 TRP cc_start: 0.7708 (m100) cc_final: 0.7461 (m100) REVERT: C 233 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: C 331 CYS cc_start: 0.7936 (m) cc_final: 0.7294 (p) REVERT: C 387 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: C 392 TYR cc_start: 0.8145 (m-80) cc_final: 0.7832 (m-80) REVERT: D 87 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6447 (mmt-90) REVERT: D 181 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7296 (mmmm) REVERT: D 197 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (p0) REVERT: D 209 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6715 (pt0) REVERT: D 257 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8112 (t70) REVERT: D 280 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8837 (mmp) REVERT: D 319 TYR cc_start: 0.8246 (t80) cc_final: 0.7886 (t80) REVERT: D 362 MET cc_start: 0.7712 (mtp) cc_final: 0.7474 (mtm) REVERT: D 376 ARG cc_start: 0.7799 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: D 394 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: D 396 LEU cc_start: 0.7792 (mp) cc_final: 0.7573 (mt) REVERT: D 403 GLU cc_start: 0.7183 (pt0) cc_final: 0.6602 (pm20) REVERT: D 432 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6447 (pt0) REVERT: D 484 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6423 (mm110) REVERT: D 519 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6320 (pp) outliers start: 108 outliers final: 48 residues processed: 308 average time/residue: 0.5097 time to fit residues: 173.6746 Evaluate side-chains 287 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN B 219 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143773 restraints weight = 16403.116| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.89 r_work: 0.3406 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15566 Z= 0.107 Angle : 0.529 8.087 21086 Z= 0.274 Chirality : 0.041 0.157 2370 Planarity : 0.004 0.041 2622 Dihedral : 8.924 80.063 2203 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 5.87 % Allowed : 32.58 % Favored : 61.55 % 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: -0.71 (0.19), residues: 1836 helix: 0.34 (0.16), residues: 1082 sheet: -0.83 (0.44), residues: 116 loop : -1.74 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.020 0.001 TYR D 405 PHE 0.018 0.001 PHE A 361 TRP 0.010 0.001 TRP B 237 HIS 0.007 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15566) covalent geometry : angle 0.52873 / 0.27 (21086) hydrogen bonds : bond 0.03768 / 2.50 ( 718) hydrogen bonds : angle 3.68235 / 2.59 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 238 time to evaluate : 0.552 Fit side-chains REVERT: A 47 ARG cc_start: 0.5196 (OUTLIER) cc_final: 0.4472 (ptt90) REVERT: A 55 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6363 (m170) REVERT: A 151 ARG cc_start: 0.6895 (tpp80) cc_final: 0.5420 (mtm180) REVERT: A 152 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7466 (tp) REVERT: A 162 MET cc_start: 0.8657 (tpt) cc_final: 0.8233 (mmm) REVERT: A 182 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5999 (mpp80) REVERT: A 233 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: A 321 ARG cc_start: 0.7543 (mmm160) cc_final: 0.7247 (mmm160) REVERT: A 331 CYS cc_start: 0.7752 (m) cc_final: 0.7144 (p) REVERT: A 335 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6062 (mpt-90) REVERT: B 66 PHE cc_start: 0.7554 (t80) cc_final: 0.7312 (t80) REVERT: B 168 MET cc_start: 0.7320 (mmt) cc_final: 0.7014 (mmm) REVERT: B 209 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6548 (pt0) REVERT: B 257 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8044 (t70) REVERT: B 360 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: B 362 MET cc_start: 0.7569 (mtp) cc_final: 0.7328 (mtm) REVERT: B 394 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 403 GLU cc_start: 0.7043 (pt0) cc_final: 0.6497 (pm20) REVERT: B 418 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6124 (mt) REVERT: B 423 GLN cc_start: 0.5980 (pm20) cc_final: 0.5592 (pm20) REVERT: B 484 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6273 (mm110) REVERT: B 519 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.6176 (pp) REVERT: C 47 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4443 (ptt90) REVERT: C 106 MET cc_start: 0.6326 (ttp) cc_final: 0.6072 (tmm) REVERT: C 151 ARG cc_start: 0.6881 (tpp80) cc_final: 0.5386 (mtm180) REVERT: C 155 GLN cc_start: 0.7600 (pm20) cc_final: 0.7353 (pm20) REVERT: C 162 MET cc_start: 0.8624 (tpt) cc_final: 0.8147 (mmm) REVERT: C 188 TRP cc_start: 0.7562 (m100) cc_final: 0.7279 (m100) REVERT: C 233 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6883 (pp20) REVERT: C 322 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 331 CYS cc_start: 0.7732 (m) cc_final: 0.7166 (p) REVERT: C 387 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: C 392 TYR cc_start: 0.7995 (m-80) cc_final: 0.7629 (m-80) REVERT: C 393 PHE cc_start: 0.8344 (m-80) cc_final: 0.8046 (m-80) REVERT: D 168 MET cc_start: 0.7308 (mmt) cc_final: 0.7004 (mmm) REVERT: D 189 ARG cc_start: 0.7396 (mtt90) cc_final: 0.7156 (mtt90) REVERT: D 209 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6558 (pt0) REVERT: D 257 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8038 (t70) REVERT: D 280 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8673 (mmp) REVERT: D 319 TYR cc_start: 0.8185 (t80) cc_final: 0.7755 (t80) REVERT: D 362 MET cc_start: 0.7465 (mtp) cc_final: 0.7214 (mtm) REVERT: D 394 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: D 403 GLU cc_start: 0.7085 (pt0) cc_final: 0.6556 (pm20) REVERT: D 426 TYR cc_start: 0.7723 (m-80) cc_final: 0.7522 (m-80) REVERT: D 484 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6306 (mm110) REVERT: D 492 ARG cc_start: 0.6449 (ttm-80) cc_final: 0.5988 (mtm180) REVERT: D 519 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6332 (pp) outliers start: 96 outliers final: 38 residues processed: 311 average time/residue: 0.6013 time to fit residues: 206.0499 Evaluate side-chains 276 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 86 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 172 optimal weight: 0.0970 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN B 219 HIS B 330 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142658 restraints weight = 16554.407| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.02 r_work: 0.3389 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15566 Z= 0.117 Angle : 0.548 8.755 21086 Z= 0.280 Chirality : 0.042 0.192 2370 Planarity : 0.004 0.044 2622 Dihedral : 8.637 80.517 2198 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.59 % Rotamer: Outliers : 5.38 % Allowed : 32.89 % Favored : 61.74 % 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 (0.19), residues: 1836 helix: 0.40 (0.16), residues: 1090 sheet: -0.84 (0.44), residues: 116 loop : -1.65 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.011 0.001 TYR B 405 PHE 0.020 0.001 PHE D 486 TRP 0.009 0.001 TRP D 273 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15566) covalent geometry : angle 0.54799 / 0.28 (21086) hydrogen bonds : bond 0.03893 / 2.58 ( 718) hydrogen bonds : angle 3.68370 / 2.59 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 224 time to evaluate : 0.632 Fit side-chains REVERT: A 47 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4474 (ptt90) REVERT: A 55 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6494 (m170) REVERT: A 151 ARG cc_start: 0.6879 (tpp80) cc_final: 0.5342 (mtm180) REVERT: A 152 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7398 (tp) REVERT: A 162 MET cc_start: 0.8616 (tpt) cc_final: 0.8165 (mmm) REVERT: A 182 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.5997 (mpp80) REVERT: A 233 GLU cc_start: 0.7244 (pm20) cc_final: 0.6933 (pm20) REVERT: A 331 CYS cc_start: 0.7744 (m) cc_final: 0.7156 (p) REVERT: A 335 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.6017 (mpt-90) REVERT: A 431 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.8160 (ptt-90) REVERT: B 66 PHE cc_start: 0.7541 (t80) cc_final: 0.7219 (t80) REVERT: B 197 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 209 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6681 (pt0) REVERT: B 257 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8066 (t70) REVERT: B 319 TYR cc_start: 0.8029 (t80) cc_final: 0.7653 (t80) REVERT: B 360 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: B 362 MET cc_start: 0.7519 (mtp) cc_final: 0.7263 (mtm) REVERT: B 394 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 403 GLU cc_start: 0.6892 (pt0) cc_final: 0.6387 (pm20) REVERT: B 418 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6120 (mt) REVERT: B 423 GLN cc_start: 0.5892 (pm20) cc_final: 0.5575 (pm20) REVERT: B 484 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6321 (mm110) REVERT: B 519 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6170 (pp) REVERT: C 47 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4627 (ptt90) REVERT: C 106 MET cc_start: 0.6298 (ttp) cc_final: 0.6049 (tmm) REVERT: C 151 ARG cc_start: 0.6933 (tpp80) cc_final: 0.5403 (mtm180) REVERT: C 162 MET cc_start: 0.8609 (tpt) cc_final: 0.8096 (mmm) REVERT: C 233 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7022 (pp20) REVERT: C 331 CYS cc_start: 0.7710 (m) cc_final: 0.7162 (p) REVERT: C 392 TYR cc_start: 0.8035 (m-80) cc_final: 0.7658 (m-80) REVERT: D 168 MET cc_start: 0.7261 (mmt) cc_final: 0.6960 (mmm) REVERT: D 189 ARG cc_start: 0.7404 (mtt90) cc_final: 0.7179 (mtt90) REVERT: D 197 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.8021 (p0) REVERT: D 209 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6692 (pt0) REVERT: D 257 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8051 (t70) REVERT: D 280 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8703 (mmp) REVERT: D 319 TYR cc_start: 0.8152 (t80) cc_final: 0.7648 (t80) REVERT: D 362 MET cc_start: 0.7439 (mtp) cc_final: 0.7175 (mtm) REVERT: D 394 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: D 403 GLU cc_start: 0.7060 (pt0) cc_final: 0.6550 (pm20) REVERT: D 461 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6181 (pp20) REVERT: D 484 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6378 (mm110) REVERT: D 492 ARG cc_start: 0.6431 (ttm-80) cc_final: 0.6001 (mtm180) REVERT: D 519 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6263 (pp) outliers start: 88 outliers final: 42 residues processed: 297 average time/residue: 0.5647 time to fit residues: 185.9214 Evaluate side-chains 273 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN B 219 HIS B 330 HIS B 512 ASN C 487 ASN D 330 HIS D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.212207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145862 restraints weight = 16504.296| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.17 r_work: 0.3376 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15566 Z= 0.110 Angle : 0.550 8.317 21086 Z= 0.279 Chirality : 0.042 0.211 2370 Planarity : 0.004 0.047 2622 Dihedral : 8.203 79.512 2198 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 4.52 % Allowed : 33.92 % Favored : 61.55 % 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: -0.51 (0.19), residues: 1836 helix: 0.46 (0.16), residues: 1110 sheet: -0.77 (0.43), residues: 116 loop : -1.66 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 321 TYR 0.021 0.001 TYR D 405 PHE 0.016 0.001 PHE A 361 TRP 0.014 0.001 TRP A 188 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15566) covalent geometry : angle 0.54955 / 0.28 (21086) hydrogen bonds : bond 0.03752 / 2.49 ( 718) hydrogen bonds : angle 3.65449 / 2.57 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 0.595 Fit side-chains REVERT: A 47 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4464 (ptt90) REVERT: A 55 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.6406 (m170) REVERT: A 151 ARG cc_start: 0.6926 (tpp80) cc_final: 0.5361 (mtm180) REVERT: A 152 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7311 (tp) REVERT: A 162 MET cc_start: 0.8748 (tpt) cc_final: 0.8287 (mmm) REVERT: A 233 GLU cc_start: 0.7251 (pm20) cc_final: 0.6961 (pm20) REVERT: A 321 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7336 (mmm160) REVERT: A 331 CYS cc_start: 0.7894 (m) cc_final: 0.7362 (p) REVERT: A 335 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6112 (mpt-90) REVERT: B 66 PHE cc_start: 0.7655 (t80) cc_final: 0.7438 (t80) REVERT: B 319 TYR cc_start: 0.8067 (t80) cc_final: 0.7641 (t80) REVERT: B 330 HIS cc_start: 0.7157 (m90) cc_final: 0.6483 (t70) REVERT: B 360 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: B 362 MET cc_start: 0.7644 (mtp) cc_final: 0.7379 (mtm) REVERT: B 376 ARG cc_start: 0.8002 (ptp-170) cc_final: 0.7600 (ptp-170) REVERT: B 394 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 403 GLU cc_start: 0.6981 (pt0) cc_final: 0.6502 (pm20) REVERT: B 418 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6476 (mt) REVERT: B 423 GLN cc_start: 0.6023 (pm20) cc_final: 0.5678 (pm20) REVERT: B 484 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6467 (mm110) REVERT: B 519 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6240 (pp) REVERT: C 47 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.4736 (ptt90) REVERT: C 106 MET cc_start: 0.6475 (ttp) cc_final: 0.6208 (tmm) REVERT: C 151 ARG cc_start: 0.6881 (tpp80) cc_final: 0.5383 (mtm180) REVERT: C 162 MET cc_start: 0.8713 (tpt) cc_final: 0.8240 (mmm) REVERT: C 233 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: C 331 CYS cc_start: 0.7865 (m) cc_final: 0.7302 (p) REVERT: C 392 TYR cc_start: 0.8186 (m-80) cc_final: 0.7624 (m-80) REVERT: C 466 ASN cc_start: 0.7001 (m-40) cc_final: 0.6784 (t0) REVERT: D 168 MET cc_start: 0.7439 (mmt) cc_final: 0.7142 (mmm) REVERT: D 237 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7435 (t60) REVERT: D 319 TYR cc_start: 0.8248 (t80) cc_final: 0.7672 (t80) REVERT: D 362 MET cc_start: 0.7577 (mtp) cc_final: 0.7293 (mtm) REVERT: D 394 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: D 403 GLU cc_start: 0.7098 (pt0) cc_final: 0.6614 (pm20) REVERT: D 418 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6640 (mt) REVERT: D 484 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6461 (mm110) REVERT: D 492 ARG cc_start: 0.6570 (ttm-80) cc_final: 0.6158 (mtm180) REVERT: D 519 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6304 (pp) outliers start: 74 outliers final: 35 residues processed: 279 average time/residue: 0.5306 time to fit residues: 164.2599 Evaluate side-chains 260 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN A 475 GLN B 219 HIS B 512 ASN C 487 ASN D 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144066 restraints weight = 16414.570| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.27 r_work: 0.3330 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15566 Z= 0.122 Angle : 0.563 8.407 21086 Z= 0.287 Chirality : 0.043 0.223 2370 Planarity : 0.004 0.050 2622 Dihedral : 7.951 80.948 2193 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.81 % Rotamer: Outliers : 4.10 % Allowed : 34.47 % Favored : 61.43 % 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: -0.43 (0.19), residues: 1836 helix: 0.52 (0.16), residues: 1098 sheet: -0.50 (0.47), residues: 102 loop : -1.60 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 321 TYR 0.011 0.001 TYR A 53 PHE 0.027 0.001 PHE D 486 TRP 0.020 0.001 TRP A 188 HIS 0.008 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15566) covalent geometry : angle 0.56311 / 0.29 (21086) hydrogen bonds : bond 0.03902 / 2.59 ( 718) hydrogen bonds : angle 3.65398 / 2.58 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.603 Fit side-chains REVERT: A 47 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.4354 (ptt90) REVERT: A 55 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6520 (m170) REVERT: A 151 ARG cc_start: 0.6949 (tpp80) cc_final: 0.6585 (mmt90) REVERT: A 152 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7306 (tp) REVERT: A 162 MET cc_start: 0.8646 (tpt) cc_final: 0.8116 (mmm) REVERT: A 233 GLU cc_start: 0.7294 (pm20) cc_final: 0.7009 (pm20) REVERT: A 321 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7278 (mmm160) REVERT: A 331 CYS cc_start: 0.7860 (m) cc_final: 0.7276 (p) REVERT: A 335 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6076 (mpt-90) REVERT: B 66 PHE cc_start: 0.7631 (t80) cc_final: 0.7429 (t80) REVERT: B 167 VAL cc_start: 0.7866 (p) cc_final: 0.7619 (m) REVERT: B 319 TYR cc_start: 0.8010 (t80) cc_final: 0.7593 (t80) REVERT: B 330 HIS cc_start: 0.7173 (m90) cc_final: 0.6426 (t70) REVERT: B 360 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: B 362 MET cc_start: 0.7669 (mtp) cc_final: 0.7396 (mtm) REVERT: B 376 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7501 (ptp-170) REVERT: B 394 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 403 GLU cc_start: 0.7004 (pt0) cc_final: 0.6428 (pm20) REVERT: B 418 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6363 (mt) REVERT: B 423 GLN cc_start: 0.5935 (pm20) cc_final: 0.5571 (pm20) REVERT: B 484 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6440 (mm110) REVERT: B 489 ARG cc_start: 0.6851 (ttp80) cc_final: 0.6558 (ttp-110) REVERT: C 47 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4517 (mmp-170) REVERT: C 151 ARG cc_start: 0.6903 (tpp80) cc_final: 0.5379 (mtm180) REVERT: C 162 MET cc_start: 0.8653 (tpt) cc_final: 0.8144 (mmm) REVERT: C 233 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: C 331 CYS cc_start: 0.7800 (m) cc_final: 0.7204 (p) REVERT: C 392 TYR cc_start: 0.8167 (m-80) cc_final: 0.7585 (m-80) REVERT: C 466 ASN cc_start: 0.6943 (m-40) cc_final: 0.6693 (t0) REVERT: D 167 VAL cc_start: 0.7795 (p) cc_final: 0.7541 (m) REVERT: D 237 TRP cc_start: 0.8390 (OUTLIER) cc_final: 0.7475 (t60) REVERT: D 319 TYR cc_start: 0.8195 (t80) cc_final: 0.7603 (t80) REVERT: D 326 ASN cc_start: 0.7523 (t0) cc_final: 0.7153 (t0) REVERT: D 362 MET cc_start: 0.7535 (mtp) cc_final: 0.7241 (mtm) REVERT: D 394 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: D 403 GLU cc_start: 0.7042 (pt0) cc_final: 0.6560 (pm20) REVERT: D 418 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6567 (mt) REVERT: D 484 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6426 (mm110) REVERT: D 492 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.6340 (mtm-85) REVERT: D 519 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6263 (pp) outliers start: 67 outliers final: 34 residues processed: 268 average time/residue: 0.5148 time to fit residues: 153.7457 Evaluate side-chains 260 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 102 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 126 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 HIS A 342 GLN A 475 GLN B 219 HIS B 512 ASN C 218 ASN C 342 GLN C 475 GLN C 487 ASN D 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146509 restraints weight = 16467.544| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.90 r_work: 0.3436 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15566 Z= 0.100 Angle : 0.543 8.998 21086 Z= 0.275 Chirality : 0.041 0.169 2370 Planarity : 0.004 0.055 2622 Dihedral : 7.367 77.660 2189 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer: Outliers : 3.36 % Allowed : 35.39 % Favored : 61.25 % 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 (0.20), residues: 1836 helix: 0.66 (0.16), residues: 1108 sheet: -0.38 (0.47), residues: 102 loop : -1.55 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.022 0.001 TYR D 405 PHE 0.018 0.001 PHE A 187 TRP 0.026 0.001 TRP A 188 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (15566) covalent geometry : angle 0.54258 / 0.27 (21086) hydrogen bonds : bond 0.03467 / 2.30 ( 718) hydrogen bonds : angle 3.54390 / 2.49 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.99 seconds wall clock time: 127 minutes 18.02 seconds (7638.02 seconds total)