Starting phenix.real_space_refine on Fri Jun 13 20:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_32597_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_32597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_32597.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_32597_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm1_32597/06_2025/7wm1_32597_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 42 Unusual residues: {' K': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 9.41, per 1000 atoms: 0.62 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.65 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: 4.79 Time building geometry restraints manager: 4.70 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 492 or resid 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.520 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:14.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 15.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.083 0.005 TRP C 73 HIS 0.009 0.001 HIS B 365 PHE 0.061 0.003 PHE B 63 TYR 0.039 0.003 TYR C 70 ARG 0.009 0.001 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.23151 ( 718) hydrogen bonds : angle 8.20439 ( 2064) covalent geometry : bond 0.01189 (15566) covalent geometry : angle 1.24805 (21086) *********************** 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 : 1.661 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.3386 (OUTLIER) cc_final: 0.2968 (mtmm) REVERT: A 47 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4458 (ptt180) REVERT: A 54 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7317 (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: 0.6912 (pp20) REVERT: A 322 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 342 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7464 (mm-40) REVERT: A 356 SER cc_start: 0.8771 (p) cc_final: 0.8436 (m) REVERT: A 368 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7283 (t70) REVERT: A 429 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6731 (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: 0.7216 (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: 0.7136 (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: 0.5908 (OUTLIER) cc_final: 0.5209 (t80) REVERT: D 338 MET cc_start: 0.6954 (tpp) cc_final: 0.6639 (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: 1.1063 time to fit residues: 622.5015 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 : 1.365 ------------------------------------------------------------------------------- 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 153 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 218 ASN A 323 GLN A 342 GLN 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 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 491 HIS D 219 HIS D 299 ASN D 330 HIS D 436 GLN D 501 HIS D 502 HIS D 509 GLN D 522 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.209077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144085 restraints weight = 16351.788| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.25 r_work: 0.3354 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15566 Z= 0.131 Angle : 0.616 8.056 21086 Z= 0.325 Chirality : 0.043 0.177 2370 Planarity : 0.005 0.043 2622 Dihedral : 13.047 111.723 2360 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.70 % Allowed : 28.61 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1836 helix: -1.35 (0.15), residues: 1052 sheet: -1.55 (0.41), residues: 122 loop : -2.17 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 60 HIS 0.007 0.001 HIS D 365 PHE 0.019 0.001 PHE B 486 TYR 0.020 0.002 TYR A 334 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 718) hydrogen bonds : angle 4.51289 ( 2064) covalent geometry : bond 0.00288 (15566) covalent geometry : angle 0.61576 (21086) *********************** 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 383 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 257 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5491 (mmt-90) REVERT: A 47 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4471 (ptt90) REVERT: A 51 SER cc_start: 0.7737 (OUTLIER) cc_final: 0.7497 (t) REVERT: A 55 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.6109 (m170) REVERT: A 151 ARG cc_start: 0.7188 (tpp80) cc_final: 0.5640 (mtm180) REVERT: A 155 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6053 (tp40) REVERT: A 168 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 233 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: A 321 ARG cc_start: 0.7391 (mmm160) cc_final: 0.7147 (mmm160) REVERT: A 343 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.5465 (tp40) REVERT: A 431 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7349 (ptt180) REVERT: B 168 MET cc_start: 0.7629 (mmt) cc_final: 0.7324 (mmm) REVERT: B 209 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6590 (pt0) REVERT: B 319 TYR cc_start: 0.8221 (t80) cc_final: 0.7919 (t80) REVERT: B 394 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7792 (tm130) REVERT: B 403 GLU cc_start: 0.6649 (pt0) cc_final: 0.6121 (pp20) REVERT: B 418 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6468 (mt) REVERT: B 461 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5978 (pp20) REVERT: B 484 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6695 (mm-40) REVERT: B 519 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6177 (pp) REVERT: C 47 ARG cc_start: 0.4980 (OUTLIER) cc_final: 0.4665 (ptt180) REVERT: C 55 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.6584 (m170) REVERT: C 151 ARG cc_start: 0.7300 (tpp80) cc_final: 0.6825 (mmt90) REVERT: C 155 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6096 (tp40) REVERT: C 188 TRP cc_start: 0.7861 (m100) cc_final: 0.7590 (m100) REVERT: C 233 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: C 321 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7379 (mmm160) REVERT: C 343 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5531 (tp40) REVERT: C 392 TYR cc_start: 0.8112 (m-80) cc_final: 0.7817 (m-80) REVERT: C 429 ILE cc_start: 0.7301 (mp) cc_final: 0.7063 (tt) REVERT: C 431 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7605 (ptm-80) REVERT: C 448 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7536 (ptp90) REVERT: D 168 MET cc_start: 0.7640 (mmt) cc_final: 0.7306 (mmm) REVERT: D 209 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6470 (pt0) REVERT: D 319 TYR cc_start: 0.8310 (t80) cc_final: 0.7758 (t80) REVERT: D 338 MET cc_start: 0.6096 (tpp) cc_final: 0.5856 (tpt) REVERT: D 367 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6935 (mm110) REVERT: D 394 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: D 403 GLU cc_start: 0.6525 (pt0) cc_final: 0.6063 (pp20) REVERT: D 418 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6388 (mt) REVERT: D 432 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7505 (pt0) REVERT: D 484 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6411 (tp-100) REVERT: D 519 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6250 (pp) outliers start: 126 outliers final: 37 residues processed: 356 average time/residue: 1.1946 time to fit residues: 471.4205 Evaluate side-chains 273 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 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 461 GLU 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 55 HIS 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 337 ASP Chi-restraints excluded: chain C residue 343 GLN 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 474 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 134 ILE 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 76 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 81 HIS B 219 HIS B 352 ASN C 487 ASN D 81 HIS D 219 HIS D 352 ASN D 522 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.205534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137334 restraints weight = 16346.090| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.20 r_work: 0.3311 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15566 Z= 0.235 Angle : 0.663 8.451 21086 Z= 0.351 Chirality : 0.047 0.181 2370 Planarity : 0.005 0.048 2622 Dihedral : 11.427 100.002 2232 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 8.56 % Allowed : 28.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 1836 helix: -0.90 (0.15), residues: 1078 sheet: -0.79 (0.46), residues: 106 loop : -2.07 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 273 HIS 0.009 0.001 HIS D 365 PHE 0.028 0.002 PHE D 110 TYR 0.019 0.002 TYR D 405 ARG 0.005 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.05551 ( 718) hydrogen bonds : angle 4.37109 ( 2064) covalent geometry : bond 0.00566 (15566) covalent geometry : angle 0.66264 (21086) *********************** 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 377 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 237 time to evaluate : 1.570 Fit side-chains REVERT: A 47 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4477 (ptt90) REVERT: A 55 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.6273 (m170) REVERT: A 151 ARG cc_start: 0.7089 (tpp80) cc_final: 0.5578 (mtm180) REVERT: A 155 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6724 (tp-100) REVERT: A 182 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5974 (mpp80) REVERT: A 233 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: A 238 MET cc_start: 0.8012 (tmt) cc_final: 0.7809 (tmt) REVERT: A 331 CYS cc_start: 0.7939 (m) cc_final: 0.7283 (p) REVERT: A 429 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.6002 (tt) REVERT: A 431 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7080 (ptp-110) REVERT: B 66 PHE cc_start: 0.7791 (t80) cc_final: 0.7585 (t80) REVERT: B 140 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 197 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8226 (p0) REVERT: B 209 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6547 (pt0) REVERT: B 319 TYR cc_start: 0.8221 (t80) cc_final: 0.7976 (t80) REVERT: B 339 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6245 (ttm110) REVERT: B 360 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: B 394 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: B 403 GLU cc_start: 0.6795 (pt0) cc_final: 0.6000 (pm20) REVERT: B 431 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6773 (mpt) REVERT: B 461 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6300 (pp20) REVERT: B 484 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6592 (tp-100) REVERT: B 512 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6797 (t0) REVERT: B 519 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6310 (pp) REVERT: C 47 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.4571 (ptt90) REVERT: C 55 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6709 (m170) REVERT: C 106 MET cc_start: 0.6212 (ttp) cc_final: 0.5977 (tmm) REVERT: C 151 ARG cc_start: 0.7310 (tpp80) cc_final: 0.6859 (mmt90) REVERT: C 155 GLN cc_start: 0.6839 (mm-40) cc_final: 0.6553 (tp-100) REVERT: C 168 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7723 (mp) REVERT: C 182 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.6047 (mpp80) REVERT: C 188 TRP cc_start: 0.7919 (m100) cc_final: 0.7612 (m100) REVERT: C 233 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: C 248 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 331 CYS cc_start: 0.7989 (m) cc_final: 0.7208 (p) REVERT: C 343 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.5452 (tp40) REVERT: C 387 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: C 392 TYR cc_start: 0.8177 (m-80) cc_final: 0.7898 (m-80) REVERT: D 140 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7782 (p) REVERT: D 197 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (p0) REVERT: D 209 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6448 (pt0) REVERT: D 257 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7955 (t70) REVERT: D 319 TYR cc_start: 0.8249 (t80) cc_final: 0.7931 (t80) REVERT: D 334 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5699 (mmp-170) REVERT: D 394 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 403 GLU cc_start: 0.6645 (pt0) cc_final: 0.5870 (pm20) REVERT: D 432 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7383 (pt0) REVERT: D 484 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6716 (tp-100) REVERT: D 519 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6307 (pp) outliers start: 140 outliers final: 53 residues processed: 347 average time/residue: 1.1690 time to fit residues: 450.3732 Evaluate side-chains 302 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 219 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 147 GLU 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 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 430 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 55 VAL 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 272 VAL Chi-restraints excluded: chain B residue 284 ILE 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 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 461 GLU 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 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL 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 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 343 GLN 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 474 ILE Chi-restraints excluded: chain D residue 55 VAL 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 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 478 VAL 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 163 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 487 ASN B 219 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN D 81 HIS 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 = 0.4267 r_free = 0.4267 target = 0.208315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142372 restraints weight = 16309.414| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.22 r_work: 0.3344 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2831 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= 0.144 Angle : 0.572 7.858 21086 Z= 0.303 Chirality : 0.043 0.155 2370 Planarity : 0.004 0.044 2622 Dihedral : 10.104 84.332 2210 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 7.33 % Allowed : 30.26 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1836 helix: -0.32 (0.16), residues: 1070 sheet: -0.96 (0.45), residues: 116 loop : -1.90 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 273 HIS 0.008 0.001 HIS D 365 PHE 0.020 0.001 PHE D 110 TYR 0.015 0.001 TYR A 283 ARG 0.004 0.000 ARG C 374 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 718) hydrogen bonds : angle 4.02707 ( 2064) covalent geometry : bond 0.00336 (15566) covalent geometry : angle 0.57156 (21086) *********************** 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 354 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 234 time to evaluate : 2.259 Fit side-chains REVERT: A 47 ARG cc_start: 0.5079 (OUTLIER) cc_final: 0.4402 (ptt90) REVERT: A 55 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6325 (m170) REVERT: A 151 ARG cc_start: 0.6946 (tpp80) cc_final: 0.5331 (mtm180) REVERT: A 155 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6591 (tp-100) REVERT: A 162 MET cc_start: 0.8752 (tpt) cc_final: 0.8376 (mmm) REVERT: A 182 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6042 (mpp80) REVERT: A 233 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: A 321 ARG cc_start: 0.7523 (mmm160) cc_final: 0.7162 (mmm160) REVERT: A 331 CYS cc_start: 0.7910 (m) cc_final: 0.7148 (p) REVERT: A 335 ARG cc_start: 0.6502 (tpp80) cc_final: 0.6142 (mpt180) REVERT: A 343 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.5414 (tp40) REVERT: A 429 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.6027 (tt) REVERT: B 209 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6551 (pt0) REVERT: B 257 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 319 TYR cc_start: 0.8273 (t80) cc_final: 0.8052 (t80) REVERT: B 339 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6236 (ttm110) REVERT: B 360 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: B 362 MET cc_start: 0.7760 (mtp) cc_final: 0.7497 (mtm) REVERT: B 394 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: B 403 GLU cc_start: 0.6817 (pt0) cc_final: 0.6098 (pm20) REVERT: B 431 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6682 (mpt) REVERT: B 461 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6265 (pp20) REVERT: B 519 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6188 (pp) REVERT: C 47 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4451 (ptt90) REVERT: C 55 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6540 (m170) REVERT: C 106 MET cc_start: 0.6269 (ttp) cc_final: 0.6030 (tmm) REVERT: C 151 ARG cc_start: 0.7008 (tpp80) cc_final: 0.5469 (mtm180) REVERT: C 155 GLN cc_start: 0.6810 (mm-40) cc_final: 0.6513 (tp-100) REVERT: C 162 MET cc_start: 0.8705 (tpt) cc_final: 0.8290 (mmm) REVERT: C 182 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6091 (mpp80) REVERT: C 188 TRP cc_start: 0.7746 (m100) cc_final: 0.7527 (m100) REVERT: C 233 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: C 331 CYS cc_start: 0.7861 (m) cc_final: 0.7124 (p) REVERT: C 337 ASP cc_start: 0.4984 (OUTLIER) cc_final: 0.4775 (p0) REVERT: C 343 GLN cc_start: 0.5687 (OUTLIER) cc_final: 0.5242 (tp40) REVERT: C 387 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: C 392 TYR cc_start: 0.8134 (m-80) cc_final: 0.7869 (m-80) REVERT: D 209 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6530 (pt0) REVERT: D 257 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7977 (t70) REVERT: D 319 TYR cc_start: 0.8252 (t80) cc_final: 0.7920 (t80) REVERT: D 394 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: D 403 GLU cc_start: 0.6762 (pt0) cc_final: 0.6047 (pm20) REVERT: D 484 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6430 (tp-100) REVERT: D 519 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6373 (pp) outliers start: 120 outliers final: 49 residues processed: 326 average time/residue: 1.3548 time to fit residues: 489.6244 Evaluate side-chains 294 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 221 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 343 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 429 ILE 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 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET 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 372 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL 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 247 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 343 GLN 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 473 ILE Chi-restraints excluded: chain C residue 474 ILE 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 257 ASP 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 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 459 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 117 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 487 ASN B 81 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.209251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141879 restraints weight = 16549.207| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.18 r_work: 0.3336 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3071 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= 0.129 Angle : 0.549 7.948 21086 Z= 0.289 Chirality : 0.042 0.153 2370 Planarity : 0.004 0.040 2622 Dihedral : 9.572 82.364 2207 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 7.15 % Allowed : 31.23 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1836 helix: -0.03 (0.16), residues: 1074 sheet: -0.89 (0.45), residues: 116 loop : -1.78 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 273 HIS 0.007 0.001 HIS D 365 PHE 0.019 0.001 PHE B 110 TYR 0.021 0.002 TYR D 405 ARG 0.006 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 718) hydrogen bonds : angle 3.86579 ( 2064) covalent geometry : bond 0.00297 (15566) covalent geometry : angle 0.54855 (21086) *********************** 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 356 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 239 time to evaluate : 1.551 Fit side-chains REVERT: A 47 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.4392 (ptt90) REVERT: A 55 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.6345 (m170) REVERT: A 151 ARG cc_start: 0.6940 (tpp80) cc_final: 0.5389 (mtm180) REVERT: A 162 MET cc_start: 0.8723 (tpt) cc_final: 0.8284 (mmm) REVERT: A 182 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6056 (mpp80) REVERT: A 233 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6975 (pp20) REVERT: A 321 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7200 (mmm160) REVERT: A 331 CYS cc_start: 0.7894 (m) cc_final: 0.7251 (p) REVERT: A 335 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6193 (mpt-90) REVERT: A 343 GLN cc_start: 0.5366 (OUTLIER) cc_final: 0.5082 (tp40) REVERT: A 431 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7556 (tmm-80) REVERT: A 432 GLU cc_start: 0.7359 (tt0) cc_final: 0.7085 (tt0) REVERT: B 168 MET cc_start: 0.7491 (mmt) cc_final: 0.7181 (mmm) REVERT: B 197 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8227 (p0) REVERT: B 209 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6560 (pt0) REVERT: B 257 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8021 (t70) REVERT: B 319 TYR cc_start: 0.8221 (t80) cc_final: 0.7996 (t80) REVERT: B 339 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6095 (ttm110) REVERT: B 358 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5533 (mmm) REVERT: B 360 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: B 362 MET cc_start: 0.7715 (mtp) cc_final: 0.7499 (mtm) REVERT: B 394 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 403 GLU cc_start: 0.6802 (pt0) cc_final: 0.6119 (pm20) REVERT: B 412 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6185 (mm-30) REVERT: B 484 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6656 (mm110) REVERT: B 519 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6151 (pp) REVERT: C 47 ARG cc_start: 0.5126 (OUTLIER) cc_final: 0.4449 (ptt90) REVERT: C 55 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.6401 (m170) REVERT: C 106 MET cc_start: 0.6248 (ttp) cc_final: 0.6018 (tmm) REVERT: C 151 ARG cc_start: 0.6978 (tpp80) cc_final: 0.5478 (mtm180) REVERT: C 155 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6468 (tp-100) REVERT: C 162 MET cc_start: 0.8670 (tpt) cc_final: 0.8237 (mmm) REVERT: C 182 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.6072 (mpp80) REVERT: C 188 TRP cc_start: 0.7587 (m100) cc_final: 0.7374 (m100) REVERT: C 233 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7112 (pp20) REVERT: C 331 CYS cc_start: 0.7843 (m) cc_final: 0.7169 (p) REVERT: C 387 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: C 392 TYR cc_start: 0.8078 (m-80) cc_final: 0.7762 (m-80) REVERT: D 66 PHE cc_start: 0.7843 (t80) cc_final: 0.7624 (t80) REVERT: D 197 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8180 (p0) REVERT: D 209 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6530 (pt0) REVERT: D 257 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8028 (t70) REVERT: D 319 TYR cc_start: 0.8205 (t80) cc_final: 0.7873 (t80) REVERT: D 394 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: D 403 GLU cc_start: 0.6916 (pt0) cc_final: 0.6293 (pm20) REVERT: D 423 GLN cc_start: 0.6279 (pm20) cc_final: 0.6029 (pm20) REVERT: D 484 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6552 (mm110) REVERT: D 519 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6301 (pp) outliers start: 117 outliers final: 52 residues processed: 330 average time/residue: 1.1959 time to fit residues: 436.6809 Evaluate side-chains 296 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 220 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 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 343 GLN 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 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 100 SER 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 324 MET Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 372 THR 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 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 155 GLN 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 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 442 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 174 LEU 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 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 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 134 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 170 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 487 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.207022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139919 restraints weight = 16473.757| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.30 r_work: 0.3266 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15566 Z= 0.192 Angle : 0.605 7.882 21086 Z= 0.318 Chirality : 0.045 0.167 2370 Planarity : 0.004 0.043 2622 Dihedral : 9.761 85.373 2198 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 7.40 % Allowed : 31.42 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1836 helix: -0.04 (0.16), residues: 1072 sheet: -0.93 (0.45), residues: 116 loop : -1.77 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 273 HIS 0.008 0.001 HIS D 365 PHE 0.027 0.002 PHE D 110 TYR 0.013 0.002 TYR D 319 ARG 0.007 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 718) hydrogen bonds : angle 3.97163 ( 2064) covalent geometry : bond 0.00461 (15566) covalent geometry : angle 0.60451 (21086) *********************** 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 340 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 219 time to evaluate : 1.555 Fit side-chains REVERT: A 47 ARG cc_start: 0.5094 (OUTLIER) cc_final: 0.4387 (ptt90) REVERT: A 55 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6539 (m170) REVERT: A 106 MET cc_start: 0.6607 (ttp) cc_final: 0.6377 (tmm) REVERT: A 151 ARG cc_start: 0.6999 (tpp80) cc_final: 0.5468 (mtm180) REVERT: A 182 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.6094 (mpp80) REVERT: A 233 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: A 321 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7251 (mmm160) REVERT: A 331 CYS cc_start: 0.8040 (m) cc_final: 0.7382 (p) REVERT: A 335 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6365 (mpt-90) REVERT: A 356 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7617 (m) REVERT: A 431 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7439 (ptm160) REVERT: B 197 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8247 (p0) REVERT: B 209 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6736 (pt0) REVERT: B 237 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7464 (t60) REVERT: B 257 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (t70) REVERT: B 319 TYR cc_start: 0.8287 (t80) cc_final: 0.8078 (t80) REVERT: B 339 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6176 (ttm110) REVERT: B 358 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5669 (mmm) REVERT: B 360 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: B 394 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: B 403 GLU cc_start: 0.6865 (pt0) cc_final: 0.6157 (pm20) REVERT: B 432 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: B 484 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6857 (mm110) REVERT: B 519 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6277 (pp) REVERT: C 47 ARG cc_start: 0.5204 (OUTLIER) cc_final: 0.4484 (ptt90) REVERT: C 55 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6631 (m170) REVERT: C 151 ARG cc_start: 0.7139 (tpp80) cc_final: 0.5660 (mtm180) REVERT: C 162 MET cc_start: 0.8730 (tpt) cc_final: 0.8248 (mmm) REVERT: C 179 GLU cc_start: 0.7390 (tt0) cc_final: 0.7067 (tt0) REVERT: C 182 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6073 (mpp80) REVERT: C 188 TRP cc_start: 0.7725 (m100) cc_final: 0.7485 (m100) REVERT: C 233 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: C 322 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 331 CYS cc_start: 0.8019 (m) cc_final: 0.7434 (p) REVERT: C 387 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: C 392 TYR cc_start: 0.8210 (m-80) cc_final: 0.7938 (m-80) REVERT: D 197 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (p0) REVERT: D 209 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6767 (pt0) REVERT: D 257 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8093 (t70) REVERT: D 319 TYR cc_start: 0.8262 (t80) cc_final: 0.7940 (t80) REVERT: D 336 PHE cc_start: 0.4502 (OUTLIER) cc_final: 0.4082 (t80) REVERT: D 362 MET cc_start: 0.7833 (mtp) cc_final: 0.7528 (mtm) REVERT: D 394 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: D 403 GLU cc_start: 0.6916 (pt0) cc_final: 0.6277 (pm20) REVERT: D 484 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6485 (tp-100) REVERT: D 519 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6401 (pp) outliers start: 121 outliers final: 50 residues processed: 315 average time/residue: 1.1676 time to fit residues: 406.5186 Evaluate side-chains 289 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 376 VAL 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 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 164 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN 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 448 SER 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 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL 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 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 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 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 336 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 128 optimal weight: 9.9990 chunk 170 optimal weight: 0.0040 chunk 102 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 181 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN 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 = 0.4279 r_free = 0.4279 target = 0.209919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144431 restraints weight = 16414.542| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.06 r_work: 0.3382 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3286 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= 0.122 Angle : 0.546 8.860 21086 Z= 0.285 Chirality : 0.042 0.156 2370 Planarity : 0.004 0.045 2622 Dihedral : 9.180 82.747 2198 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 6.91 % Allowed : 31.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1836 helix: 0.25 (0.16), residues: 1072 sheet: -0.96 (0.44), residues: 120 loop : -1.71 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 237 HIS 0.006 0.001 HIS D 365 PHE 0.018 0.001 PHE B 110 TYR 0.021 0.001 TYR B 405 ARG 0.009 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 718) hydrogen bonds : angle 3.75488 ( 2064) covalent geometry : bond 0.00278 (15566) covalent geometry : angle 0.54558 (21086) *********************** 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 346 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 233 time to evaluate : 1.727 Fit side-chains REVERT: A 47 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.4383 (ptt90) REVERT: A 55 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6492 (m170) REVERT: A 106 MET cc_start: 0.6537 (ttp) cc_final: 0.6296 (tmm) REVERT: A 151 ARG cc_start: 0.6990 (tpp80) cc_final: 0.5438 (mtm180) REVERT: A 162 MET cc_start: 0.8780 (tpt) cc_final: 0.8347 (mmm) REVERT: A 182 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.6050 (mpp80) REVERT: A 233 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6957 (pp20) REVERT: A 321 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7305 (mmm160) REVERT: A 331 CYS cc_start: 0.7872 (m) cc_final: 0.7321 (p) REVERT: A 335 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6218 (mpt-90) REVERT: A 431 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7758 (ttp-110) REVERT: B 66 PHE cc_start: 0.7824 (t80) cc_final: 0.7593 (t80) REVERT: B 163 SER cc_start: 0.8283 (t) cc_final: 0.7684 (p) REVERT: B 197 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 257 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8107 (t70) REVERT: B 319 TYR cc_start: 0.8265 (t80) cc_final: 0.8036 (t80) REVERT: B 326 ASN cc_start: 0.7763 (t0) cc_final: 0.7392 (t0) REVERT: B 339 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6188 (ttm110) REVERT: B 360 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: B 394 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: B 403 GLU cc_start: 0.7119 (pt0) cc_final: 0.6473 (pm20) REVERT: B 432 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6520 (pt0) REVERT: B 484 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6741 (mm110) REVERT: B 519 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6302 (pp) REVERT: C 47 ARG cc_start: 0.5183 (OUTLIER) cc_final: 0.4480 (ptt90) REVERT: C 55 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.6341 (m170) REVERT: C 151 ARG cc_start: 0.7029 (tpp80) cc_final: 0.5548 (mtm180) REVERT: C 162 MET cc_start: 0.8733 (tpt) cc_final: 0.8314 (mmm) REVERT: C 188 TRP cc_start: 0.7679 (m100) cc_final: 0.7438 (m100) REVERT: C 233 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: C 322 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7383 (mt) REVERT: C 331 CYS cc_start: 0.7873 (m) cc_final: 0.7324 (p) REVERT: C 387 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: C 392 TYR cc_start: 0.8116 (m-80) cc_final: 0.7775 (m-80) REVERT: C 393 PHE cc_start: 0.8443 (m-80) cc_final: 0.8238 (m-80) REVERT: D 87 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6392 (mmt-90) REVERT: D 189 ARG cc_start: 0.7478 (mtt90) cc_final: 0.7246 (mtt90) REVERT: D 257 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8100 (t70) REVERT: D 319 TYR cc_start: 0.8321 (t80) cc_final: 0.7946 (t80) REVERT: D 376 ARG cc_start: 0.7872 (ptp-170) cc_final: 0.7478 (ptp-170) REVERT: D 394 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: D 403 GLU cc_start: 0.7208 (pt0) cc_final: 0.6649 (pm20) REVERT: D 484 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6331 (mm110) REVERT: D 519 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6364 (pp) outliers start: 113 outliers final: 50 residues processed: 320 average time/residue: 1.1914 time to fit residues: 421.7332 Evaluate side-chains 292 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 292 VAL 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 411 ILE 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 100 SER Chi-restraints excluded: chain B residue 108 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 339 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN 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 51 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 VAL 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 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 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 257 ASP 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 101 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 487 ASN B 219 HIS B 330 HIS B 512 ASN C 342 GLN C 487 ASN D 219 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 = 0.4257 r_free = 0.4257 target = 0.207483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147681 restraints weight = 16389.224| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.08 r_work: 0.3369 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15566 Z= 0.165 Angle : 0.599 8.606 21086 Z= 0.309 Chirality : 0.045 0.218 2370 Planarity : 0.004 0.046 2622 Dihedral : 9.245 84.544 2196 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 6.60 % Allowed : 31.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1836 helix: 0.20 (0.16), residues: 1076 sheet: -1.04 (0.44), residues: 120 loop : -1.69 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 273 HIS 0.008 0.001 HIS D 365 PHE 0.024 0.002 PHE B 110 TYR 0.013 0.002 TYR B 426 ARG 0.009 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 718) hydrogen bonds : angle 3.81745 ( 2064) covalent geometry : bond 0.00393 (15566) covalent geometry : angle 0.59935 (21086) *********************** 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 329 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 221 time to evaluate : 1.532 Fit side-chains REVERT: A 47 ARG cc_start: 0.5142 (OUTLIER) cc_final: 0.4357 (ptt90) REVERT: A 55 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6548 (m170) REVERT: A 106 MET cc_start: 0.6578 (ttp) cc_final: 0.6337 (tmm) REVERT: A 151 ARG cc_start: 0.7064 (tpp80) cc_final: 0.5534 (mtm180) REVERT: A 162 MET cc_start: 0.8732 (tpt) cc_final: 0.8263 (mmm) REVERT: A 182 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6049 (mpp80) REVERT: A 233 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: A 321 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7308 (mmm160) REVERT: A 331 CYS cc_start: 0.7891 (m) cc_final: 0.7309 (p) REVERT: A 335 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6292 (mpt-90) REVERT: A 356 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7489 (m) REVERT: A 431 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7739 (tmm-80) REVERT: A 432 GLU cc_start: 0.7271 (tt0) cc_final: 0.7016 (tt0) REVERT: B 197 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (p0) REVERT: B 257 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8041 (t70) REVERT: B 319 TYR cc_start: 0.8219 (t80) cc_final: 0.7950 (t80) REVERT: B 326 ASN cc_start: 0.7717 (t0) cc_final: 0.7408 (t0) REVERT: B 339 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6096 (ttm110) REVERT: B 360 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: B 394 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: B 403 GLU cc_start: 0.7164 (pt0) cc_final: 0.6569 (pm20) REVERT: B 432 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6395 (pt0) REVERT: B 484 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6795 (mm110) REVERT: B 519 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6346 (pp) REVERT: C 47 ARG cc_start: 0.5308 (OUTLIER) cc_final: 0.4632 (ptt90) REVERT: C 55 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6479 (m170) REVERT: C 151 ARG cc_start: 0.7120 (tpp80) cc_final: 0.5602 (mtm180) REVERT: C 162 MET cc_start: 0.8687 (tpt) cc_final: 0.8203 (mmm) REVERT: C 182 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6101 (mpp80) REVERT: C 187 PHE cc_start: 0.7218 (t80) cc_final: 0.6967 (t80) REVERT: C 188 TRP cc_start: 0.7683 (m100) cc_final: 0.7371 (m100) REVERT: C 322 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7427 (mt) REVERT: C 331 CYS cc_start: 0.7860 (m) cc_final: 0.7293 (p) REVERT: C 387 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: C 392 TYR cc_start: 0.8118 (m-80) cc_final: 0.7840 (m-80) REVERT: D 197 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8163 (p0) REVERT: D 257 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8018 (t70) REVERT: D 319 TYR cc_start: 0.8288 (t80) cc_final: 0.7896 (t80) REVERT: D 336 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.4083 (t80) REVERT: D 362 MET cc_start: 0.7761 (mtp) cc_final: 0.7448 (mtm) REVERT: D 376 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7418 (ptp-170) REVERT: D 394 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: D 403 GLU cc_start: 0.7198 (pt0) cc_final: 0.6607 (pm20) REVERT: D 432 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6405 (pt0) REVERT: D 435 LEU cc_start: 0.7924 (mm) cc_final: 0.7647 (mt) REVERT: D 484 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6527 (mm110) REVERT: D 519 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6432 (pp) outliers start: 108 outliers final: 57 residues processed: 313 average time/residue: 1.1240 time to fit residues: 392.6461 Evaluate side-chains 300 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 356 SER 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 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE 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 339 ARG 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 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 448 SER 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 51 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 69 VAL 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 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 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 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 164 VAL 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 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 132 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 487 ASN B 219 HIS B 330 HIS B 512 ASN C 342 GLN C 487 ASN D 219 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 = 0.4266 r_free = 0.4266 target = 0.208568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138674 restraints weight = 16340.854| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.91 r_work: 0.3361 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 15566 Z= 0.138 Angle : 0.584 8.342 21086 Z= 0.301 Chirality : 0.044 0.215 2370 Planarity : 0.004 0.048 2622 Dihedral : 8.938 83.665 2196 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.48 % Rotamer: Outliers : 5.99 % Allowed : 32.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1836 helix: 0.33 (0.16), residues: 1072 sheet: -1.05 (0.44), residues: 120 loop : -1.61 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 237 HIS 0.007 0.001 HIS B 365 PHE 0.019 0.001 PHE B 110 TYR 0.021 0.001 TYR B 405 ARG 0.010 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 718) hydrogen bonds : angle 3.72732 ( 2064) covalent geometry : bond 0.00332 (15566) covalent geometry : angle 0.58418 (21086) *********************** 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 316 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 1.945 Fit side-chains REVERT: A 47 ARG cc_start: 0.5168 (OUTLIER) cc_final: 0.4366 (ptt90) REVERT: A 55 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6485 (m170) REVERT: A 106 MET cc_start: 0.6393 (ttp) cc_final: 0.6167 (tmm) REVERT: A 151 ARG cc_start: 0.7056 (tpp80) cc_final: 0.5503 (mtm180) REVERT: A 162 MET cc_start: 0.8633 (tpt) cc_final: 0.8175 (mmm) REVERT: A 182 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6051 (mpp80) REVERT: A 233 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6824 (pp20) REVERT: A 321 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7276 (mmm160) REVERT: A 331 CYS cc_start: 0.7675 (m) cc_final: 0.7116 (p) REVERT: A 335 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6199 (mpt-90) REVERT: A 431 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7735 (tmm-80) REVERT: A 432 GLU cc_start: 0.7249 (tt0) cc_final: 0.6960 (tt0) REVERT: B 197 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8085 (p0) REVERT: B 257 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7977 (t70) REVERT: B 319 TYR cc_start: 0.8135 (t80) cc_final: 0.7902 (t80) REVERT: B 326 ASN cc_start: 0.7604 (t0) cc_final: 0.7274 (t0) REVERT: B 339 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5789 (ttm110) REVERT: B 360 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: B 366 MET cc_start: 0.7189 (tpp) cc_final: 0.6396 (tmm) REVERT: B 394 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: B 403 GLU cc_start: 0.7113 (pt0) cc_final: 0.6527 (pm20) REVERT: B 484 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6632 (mm110) REVERT: B 519 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6293 (pp) REVERT: C 47 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.4518 (mmp-170) REVERT: C 55 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6415 (m170) REVERT: C 151 ARG cc_start: 0.6997 (tpp80) cc_final: 0.5504 (mtm180) REVERT: C 162 MET cc_start: 0.8584 (tpt) cc_final: 0.8112 (mmm) REVERT: C 188 TRP cc_start: 0.7617 (m100) cc_final: 0.7373 (m100) REVERT: C 303 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7062 (ptm160) REVERT: C 321 ARG cc_start: 0.7533 (mmm160) cc_final: 0.7330 (mmm160) REVERT: C 331 CYS cc_start: 0.7704 (m) cc_final: 0.7178 (p) REVERT: C 387 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: C 392 TYR cc_start: 0.8023 (m-80) cc_final: 0.7710 (m-80) REVERT: D 197 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8064 (p0) REVERT: D 257 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8036 (t70) REVERT: D 319 TYR cc_start: 0.8199 (t80) cc_final: 0.7754 (t80) REVERT: D 336 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.4062 (t80) REVERT: D 366 MET cc_start: 0.7132 (ttp) cc_final: 0.6927 (tmm) REVERT: D 376 ARG cc_start: 0.7677 (ptp-170) cc_final: 0.7266 (ptp-170) REVERT: D 394 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: D 403 GLU cc_start: 0.7130 (pt0) cc_final: 0.6548 (pm20) REVERT: D 432 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6469 (pt0) REVERT: D 435 LEU cc_start: 0.7807 (mm) cc_final: 0.7548 (mt) REVERT: D 484 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6405 (mm110) REVERT: D 519 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6317 (pp) outliers start: 98 outliers final: 54 residues processed: 301 average time/residue: 1.2103 time to fit residues: 404.3068 Evaluate side-chains 286 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 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 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 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE 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 339 ARG 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 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 SER 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 51 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 303 ARG 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 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 164 VAL 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 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 154 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 487 ASN B 219 HIS B 330 HIS B 512 ASN C 342 GLN C 487 ASN D 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.207076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139665 restraints weight = 16512.341| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.15 r_work: 0.3338 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15566 Z= 0.181 Angle : 0.620 8.574 21086 Z= 0.320 Chirality : 0.046 0.271 2370 Planarity : 0.004 0.049 2622 Dihedral : 9.111 84.872 2195 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 5.81 % Allowed : 32.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1836 helix: 0.19 (0.16), residues: 1086 sheet: -0.80 (0.47), residues: 102 loop : -1.61 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 188 HIS 0.008 0.001 HIS B 365 PHE 0.031 0.002 PHE B 486 TYR 0.012 0.002 TYR A 410 ARG 0.010 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 718) hydrogen bonds : angle 3.85107 ( 2064) covalent geometry : bond 0.00438 (15566) covalent geometry : angle 0.62036 (21086) ********************** 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 302 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 207 time to evaluate : 1.634 Fit side-chains REVERT: A 47 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4372 (ptt90) REVERT: A 55 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.6721 (m170) REVERT: A 106 MET cc_start: 0.6603 (ttp) cc_final: 0.6374 (tmm) REVERT: A 151 ARG cc_start: 0.7122 (tpp80) cc_final: 0.5594 (mtm180) REVERT: A 162 MET cc_start: 0.8764 (tpt) cc_final: 0.8306 (mmm) REVERT: A 182 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.6064 (mpp80) REVERT: A 233 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6939 (pp20) REVERT: A 321 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7303 (mmm160) REVERT: A 331 CYS cc_start: 0.7861 (m) cc_final: 0.7309 (p) REVERT: A 335 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6290 (mpt-90) REVERT: A 431 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7768 (tmm-80) REVERT: A 432 GLU cc_start: 0.7217 (tt0) cc_final: 0.6928 (tt0) REVERT: B 197 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8180 (p0) REVERT: B 257 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8106 (t70) REVERT: B 319 TYR cc_start: 0.8291 (t80) cc_final: 0.8035 (t80) REVERT: B 330 HIS cc_start: 0.7342 (m90) cc_final: 0.6599 (t70) REVERT: B 339 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5915 (ttm110) REVERT: B 360 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: B 366 MET cc_start: 0.7428 (tpp) cc_final: 0.6609 (tmm) REVERT: B 394 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: B 403 GLU cc_start: 0.7256 (pt0) cc_final: 0.6659 (pm20) REVERT: B 484 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6792 (mm110) REVERT: B 519 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6444 (pp) REVERT: C 47 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4512 (mmp-170) REVERT: C 55 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6536 (m170) REVERT: C 151 ARG cc_start: 0.7022 (tpp80) cc_final: 0.5561 (mtm180) REVERT: C 162 MET cc_start: 0.8728 (tpt) cc_final: 0.8260 (mmm) REVERT: C 303 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7128 (ptm160) REVERT: C 331 CYS cc_start: 0.7919 (m) cc_final: 0.7398 (p) REVERT: C 387 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: C 392 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80) REVERT: D 197 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (p0) REVERT: D 257 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (t70) REVERT: D 319 TYR cc_start: 0.8353 (t80) cc_final: 0.7979 (t80) REVERT: D 336 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.4123 (t80) REVERT: D 362 MET cc_start: 0.7685 (mtp) cc_final: 0.7371 (mtm) REVERT: D 394 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: D 403 GLU cc_start: 0.7260 (pt0) cc_final: 0.6666 (pm20) REVERT: D 432 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6521 (pt0) REVERT: D 435 LEU cc_start: 0.7995 (mm) cc_final: 0.7742 (mt) REVERT: D 484 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6553 (mm110) REVERT: D 489 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6930 (ttp-110) REVERT: D 519 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6435 (pp) outliers start: 95 outliers final: 56 residues processed: 293 average time/residue: 1.1518 time to fit residues: 375.1870 Evaluate side-chains 282 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG 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 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE 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 339 ARG 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 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 SER 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 51 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 THR 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 303 ARG 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 433 VAL 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 164 VAL 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 284 ILE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 487 ASN B 219 HIS B 512 ASN C 342 GLN C 487 ASN D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.208465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138511 restraints weight = 16382.669| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.92 r_work: 0.3365 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 15566 Z= 0.144 Angle : 0.593 8.220 21086 Z= 0.305 Chirality : 0.044 0.253 2370 Planarity : 0.004 0.049 2622 Dihedral : 8.893 84.007 2195 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 5.56 % Allowed : 32.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1836 helix: 0.33 (0.16), residues: 1082 sheet: -0.72 (0.48), residues: 102 loop : -1.58 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 188 HIS 0.007 0.001 HIS D 365 PHE 0.020 0.001 PHE B 110 TYR 0.021 0.001 TYR B 405 ARG 0.011 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 718) hydrogen bonds : angle 3.76647 ( 2064) covalent geometry : bond 0.00347 (15566) covalent geometry : angle 0.59253 (21086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16167.10 seconds wall clock time: 278 minutes 39.26 seconds (16719.26 seconds total)