Starting phenix.real_space_refine on Thu Feb 5 05:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm1_32597/02_2026/7wm1_32597_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 72 5.16 5 C 9948 2.51 5 N 2516 2.21 5 O 2654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15197 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "B" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "C" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "D" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 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: 2.76, per 1000 atoms: 0.18 Number of scatterers: 15197 At special positions: 0 Unit cell: (115.271, 113.117, 123.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 72 16.00 P 4 15.00 O 2654 8.00 N 2516 7.00 C 9948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 528.7 milliseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 12 sheets defined 58.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.575A pdb=" N TRP A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 107 removed outlier: 3.575A pdb=" N ILE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 4.361A pdb=" N PHE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.717A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.795A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 215 removed outlier: 4.111A pdb=" N ALA A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.599A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 290 removed outlier: 3.642A pdb=" N MET A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.603A pdb=" N ARG A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.763A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.798A pdb=" N GLU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.609A pdb=" N LEU A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 369 removed outlier: 3.585A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.662A pdb=" N GLU A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 467 through 476 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 83 through 110 removed outlier: 3.835A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.633A pdb=" N VAL B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 163 through 173 removed outlier: 4.218A pdb=" N VAL B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU B 199 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 203 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.635A pdb=" N LYS B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.547A pdb=" N ARG B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 288 removed outlier: 3.604A pdb=" N GLY B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 277 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.800A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 352 removed outlier: 3.765A pdb=" N SER B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 removed outlier: 3.686A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.632A pdb=" N HIS B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.955A pdb=" N ILE B 401 " --> pdb=" O PHE B 397 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 474 through 481 removed outlier: 4.015A pdb=" N VAL B 478 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 518 through 526 Processing helix chain 'C' and resid 54 through 81 removed outlier: 3.515A pdb=" N ALA C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 107 removed outlier: 3.574A pdb=" N ILE C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 132 removed outlier: 4.306A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.717A pdb=" N ARG C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.795A pdb=" N GLY C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 192 through 215 removed outlier: 3.682A pdb=" N CYS C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 253 removed outlier: 3.599A pdb=" N TYR C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 290 removed outlier: 3.641A pdb=" N MET C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.604A pdb=" N ARG C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.763A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.736A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.609A pdb=" N LEU C 350 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 369 removed outlier: 3.585A pdb=" N SER C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.661A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 467 through 476 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 83 through 110 removed outlier: 3.835A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.634A pdb=" N VAL D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 163 through 173 removed outlier: 4.217A pdb=" N VAL D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU D 199 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 203 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.634A pdb=" N LYS D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 251 removed outlier: 3.535A pdb=" N LEU D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 288 removed outlier: 3.603A pdb=" N GLY D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 277 " --> pdb=" O TRP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.801A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 4.076A pdb=" N ASP D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 376 removed outlier: 3.685A pdb=" N ARG D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 removed outlier: 3.633A pdb=" N HIS D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.956A pdb=" N ILE D 401 " --> pdb=" O PHE D 397 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 403 " --> pdb=" O SER D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'D' and resid 474 through 481 removed outlier: 4.015A pdb=" N VAL D 478 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 518 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.755A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 433 removed outlier: 3.872A pdb=" N SER A 428 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 421 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'B' and resid 424 through 427 removed outlier: 7.040A pdb=" N GLN B 495 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 432 through 434 removed outlier: 6.789A pdb=" N VAL B 488 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 451 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS B 466 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 453 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 462 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.755A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 428 through 429 removed outlier: 3.872A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'D' and resid 424 through 427 removed outlier: 7.040A pdb=" N GLN D 495 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 432 through 434 removed outlier: 6.787A pdb=" N VAL D 488 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 451 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS D 466 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 453 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 462 " --> pdb=" O ALA D 455 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 26 1.15 - 1.31: 2358 1.31 - 1.48: 6419 1.48 - 1.65: 6637 1.65 - 1.81: 126 Bond restraints: 15566 Sorted by residual: bond pdb=" C TRP C 73 " pdb=" O TRP C 73 " ideal model delta sigma weight residual 1.236 0.982 0.254 1.15e-02 7.56e+03 4.89e+02 bond pdb=" C ALA C 72 " pdb=" O ALA C 72 " ideal model delta sigma weight residual 1.237 0.982 0.255 1.16e-02 7.43e+03 4.83e+02 bond pdb=" C THR C 71 " pdb=" O THR C 71 " ideal model delta sigma weight residual 1.236 1.010 0.226 1.28e-02 6.10e+03 3.11e+02 bond pdb=" C PRO C 76 " pdb=" O PRO C 76 " ideal model delta sigma weight residual 1.237 1.041 0.196 1.26e-02 6.30e+03 2.42e+02 bond pdb=" C PHE C 77 " pdb=" O PHE C 77 " ideal model delta sigma weight residual 1.236 1.044 0.192 1.26e-02 6.30e+03 2.33e+02 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 20847 4.63 - 9.25: 205 9.25 - 13.88: 22 13.88 - 18.51: 9 18.51 - 23.14: 3 Bond angle restraints: 21086 Sorted by residual: angle pdb=" C LEU D 60 " pdb=" N PRO D 61 " pdb=" CA PRO D 61 " ideal model delta sigma weight residual 119.90 135.40 -15.50 1.05e+00 9.07e-01 2.18e+02 angle pdb=" C TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta sigma weight residual 110.88 87.74 23.14 1.57e+00 4.06e-01 2.17e+02 angle pdb=" C TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta sigma weight residual 110.88 87.77 23.11 1.57e+00 4.06e-01 2.17e+02 angle pdb=" O MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 122.39 101.53 20.86 1.48e+00 4.57e-01 1.99e+02 angle pdb=" CA MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 118.44 135.44 -17.00 1.41e+00 5.03e-01 1.45e+02 ... (remaining 21081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 8266 26.62 - 53.25: 792 53.25 - 79.87: 130 79.87 - 106.49: 16 106.49 - 133.11: 2 Dihedral angle restraints: 9206 sinusoidal: 3770 harmonic: 5436 Sorted by residual: dihedral pdb=" C TYR A 57 " pdb=" N TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta harmonic sigma weight residual -122.60 -95.90 -26.70 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C TYR C 57 " pdb=" N TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta harmonic sigma weight residual -122.60 -95.92 -26.68 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C ASP C 54 " pdb=" N ASP C 54 " pdb=" CA ASP C 54 " pdb=" CB ASP C 54 " ideal model delta harmonic sigma weight residual -122.60 -144.47 21.87 0 2.50e+00 1.60e-01 7.65e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2275 0.170 - 0.340: 71 0.340 - 0.510: 19 0.510 - 0.680: 2 0.680 - 0.851: 3 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA PRO C 76 " pdb=" N PRO C 76 " pdb=" C PRO C 76 " pdb=" CB PRO C 76 " both_signs ideal model delta sigma weight residual False 2.72 1.87 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA ASP C 54 " pdb=" N ASP C 54 " pdb=" C ASP C 54 " pdb=" CB ASP C 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA ASP A 54 " pdb=" N ASP A 54 " pdb=" C ASP A 54 " pdb=" CB ASP A 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 ... (remaining 2367 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 701 " -0.252 2.00e-02 2.50e+03 2.37e-01 5.63e+02 pdb=" C29 POV B 701 " 0.308 2.00e-02 2.50e+03 pdb="C210 POV B 701 " 0.153 2.00e-02 2.50e+03 pdb="C211 POV B 701 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 901 " 0.141 2.00e-02 2.50e+03 1.41e-01 1.99e+02 pdb=" C29 POV C 901 " -0.139 2.00e-02 2.50e+03 pdb="C210 POV C 901 " -0.143 2.00e-02 2.50e+03 pdb="C211 POV C 901 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " 0.119 2.00e-02 2.50e+03 1.18e-01 1.39e+02 pdb=" C29 POV D 701 " -0.127 2.00e-02 2.50e+03 pdb="C210 POV D 701 " -0.109 2.00e-02 2.50e+03 pdb="C211 POV D 701 " 0.116 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 663 2.69 - 3.30: 17049 3.30 - 3.92: 27668 3.92 - 4.53: 39251 4.53 - 5.14: 61322 Nonbonded interactions: 145953 Sorted by model distance: nonbonded pdb=" N ASP D 344 " pdb=" OD1 ASP D 344 " model vdw 2.080 3.120 nonbonded pdb=" O THR D 288 " pdb=" OG1 THR D 289 " model vdw 2.144 3.040 nonbonded pdb=" O THR B 288 " pdb=" OG1 THR B 289 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" O22 POV A 901 " model vdw 2.200 3.040 nonbonded pdb=" N ASP B 452 " pdb=" OD1 ASP B 452 " model vdw 2.206 3.120 ... (remaining 145948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 901) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- 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 : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 15.89 % Allowed : 23.78 % Favored : 60.33 % Cbeta Deviations : 1.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.16), residues: 1836 helix: -2.85 (0.12), residues: 1044 sheet: -1.83 (0.46), residues: 100 loop : -2.87 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 226 TYR 0.039 0.003 TYR C 70 PHE 0.061 0.003 PHE B 63 TRP 0.083 0.005 TRP C 73 HIS 0.009 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.01189 (15566) covalent geometry : angle 1.24805 (21086) hydrogen bonds : bond 0.23151 ( 718) hydrogen bonds : angle 8.20439 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 294 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.3386 (OUTLIER) cc_final: 0.2971 (mtmm) REVERT: A 47 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4459 (ptt180) REVERT: A 54 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7318 (p0) REVERT: A 55 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7224 (m170) REVERT: A 233 GLU cc_start: 0.7125 (pm20) cc_final: 0.6911 (pp20) REVERT: A 322 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 356 SER cc_start: 0.8771 (p) cc_final: 0.8438 (m) REVERT: A 368 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7285 (t70) REVERT: A 429 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6730 (tt) REVERT: B 319 TYR cc_start: 0.7854 (t80) cc_final: 0.7499 (t80) REVERT: B 324 MET cc_start: 0.8008 (tpp) cc_final: 0.7705 (tpt) REVERT: B 394 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (tm130) REVERT: B 418 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 519 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6379 (pp) REVERT: B 520 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7217 (mm) REVERT: C 44 LYS cc_start: 0.3295 (OUTLIER) cc_final: 0.2990 (mtmt) REVERT: C 47 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4660 (ptt180) REVERT: C 55 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7135 (m170) REVERT: C 151 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7030 (mmt90) REVERT: C 188 TRP cc_start: 0.8076 (m100) cc_final: 0.7737 (m100) REVERT: C 322 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 342 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7637 (mm-40) REVERT: C 368 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6975 (p0) REVERT: C 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 392 TYR cc_start: 0.7968 (m-80) cc_final: 0.7707 (m-80) REVERT: C 429 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6756 (tt) REVERT: C 448 ARG cc_start: 0.7319 (ptp-110) cc_final: 0.7068 (ptp90) REVERT: D 167 VAL cc_start: 0.8407 (p) cc_final: 0.8195 (m) REVERT: D 280 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: D 319 TYR cc_start: 0.7779 (t80) cc_final: 0.7447 (t80) REVERT: D 324 MET cc_start: 0.7990 (tpp) cc_final: 0.7710 (tpt) REVERT: D 336 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5208 (t80) REVERT: D 338 MET cc_start: 0.6954 (tpp) cc_final: 0.6640 (ttm) REVERT: D 359 ARG cc_start: 0.6590 (ttm110) cc_final: 0.6229 (ttm110) REVERT: D 520 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7386 (mm) outliers start: 260 outliers final: 89 residues processed: 504 average time/residue: 0.4675 time to fit residues: 261.5936 Evaluate side-chains 328 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 218 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 218 ASN A 323 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 461 GLN A 487 ASN A 491 HIS B 219 HIS B 299 ASN B 330 HIS B 436 GLN B 501 HIS B 502 HIS B 522 ASN C 97 ASN C 218 ASN C 323 GLN C 342 GLN C 378 ASN C 461 GLN C 487 ASN C 491 HIS D 219 HIS D 299 ASN D 330 HIS D 436 GLN D 501 HIS D 502 HIS D 509 GLN D 522 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.207860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149668 restraints weight = 16395.330| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.09 r_work: 0.3431 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2341 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= 0.134 Angle : 0.615 8.316 21086 Z= 0.325 Chirality : 0.043 0.187 2370 Planarity : 0.005 0.044 2622 Dihedral : 12.992 111.332 2360 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.64 % Allowed : 28.79 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.18), residues: 1836 helix: -1.38 (0.15), residues: 1056 sheet: -1.19 (0.43), residues: 110 loop : -2.17 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.020 0.002 TYR A 334 PHE 0.019 0.002 PHE B 486 TRP 0.014 0.002 TRP A 60 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00294 (15566) covalent geometry : angle 0.61470 (21086) hydrogen bonds : bond 0.04831 ( 718) hydrogen bonds : angle 4.54751 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 258 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5720 (mpp-170) REVERT: A 47 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4456 (ptt90) REVERT: A 51 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7565 (t) REVERT: A 55 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6148 (m170) REVERT: A 151 ARG cc_start: 0.7191 (tpp80) cc_final: 0.5660 (mtm180) REVERT: A 155 GLN cc_start: 0.6674 (mm-40) cc_final: 0.6029 (tp40) REVERT: A 168 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7980 (mp) REVERT: A 233 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: A 321 ARG cc_start: 0.7359 (mmm160) cc_final: 0.7117 (mmm160) REVERT: A 343 GLN cc_start: 0.5838 (OUTLIER) cc_final: 0.5498 (tp40) REVERT: A 367 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: B 168 MET cc_start: 0.7505 (mmt) cc_final: 0.7193 (mmm) REVERT: B 209 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6417 (pt0) REVERT: B 319 TYR cc_start: 0.8139 (t80) cc_final: 0.7872 (t80) REVERT: B 394 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7699 (tm130) REVERT: B 403 GLU cc_start: 0.6639 (pt0) cc_final: 0.6101 (pp20) REVERT: B 418 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6405 (mt) REVERT: B 461 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: B 484 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6667 (mm-40) REVERT: B 512 ASN cc_start: 0.6937 (m-40) cc_final: 0.6669 (t0) REVERT: B 519 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6210 (pp) REVERT: C 47 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.4514 (ptt90) REVERT: C 55 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6682 (m170) REVERT: C 151 ARG cc_start: 0.7305 (tpp80) cc_final: 0.6819 (mmt90) REVERT: C 155 GLN cc_start: 0.6645 (mm-40) cc_final: 0.6067 (tp40) REVERT: C 188 TRP cc_start: 0.7818 (m100) cc_final: 0.7538 (m100) REVERT: C 233 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: C 321 ARG cc_start: 0.7582 (mmm160) cc_final: 0.7379 (mmm160) REVERT: C 342 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6882 (tp-100) REVERT: C 343 GLN cc_start: 0.5952 (OUTLIER) cc_final: 0.5564 (tp40) REVERT: C 392 TYR cc_start: 0.8058 (m-80) cc_final: 0.7756 (m-80) REVERT: C 429 ILE cc_start: 0.7314 (mp) cc_final: 0.7067 (tt) REVERT: C 431 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7649 (ptm-80) REVERT: C 448 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7550 (ptp90) REVERT: D 168 MET cc_start: 0.7512 (mmt) cc_final: 0.7168 (mmm) REVERT: D 209 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6310 (pt0) REVERT: D 280 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8742 (mmp) REVERT: D 319 TYR cc_start: 0.8226 (t80) cc_final: 0.7686 (t80) REVERT: D 338 MET cc_start: 0.6157 (tpp) cc_final: 0.5931 (tpt) REVERT: D 367 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6910 (mm110) REVERT: D 394 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: D 403 GLU cc_start: 0.6515 (pt0) cc_final: 0.6046 (pp20) REVERT: D 418 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6325 (mt) REVERT: D 432 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7477 (pt0) REVERT: D 484 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6369 (tp-100) REVERT: D 519 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6257 (pp) outliers start: 125 outliers final: 40 residues processed: 357 average time/residue: 0.4926 time to fit residues: 194.5065 Evaluate side-chains 280 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 367 MET 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 478 VAL 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 284 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 342 GLN 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 383 GLN 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 280 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 352 ASN C 487 ASN D 219 HIS D 352 ASN D 522 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.210127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143148 restraints weight = 16488.046| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.20 r_work: 0.3372 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15566 Z= 0.118 Angle : 0.552 8.842 21086 Z= 0.290 Chirality : 0.042 0.148 2370 Planarity : 0.004 0.040 2622 Dihedral : 10.633 90.698 2237 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.91 % Allowed : 30.01 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1836 helix: -0.56 (0.16), residues: 1068 sheet: -1.06 (0.43), residues: 116 loop : -1.89 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 374 TYR 0.020 0.001 TYR D 405 PHE 0.016 0.001 PHE B 110 TRP 0.011 0.001 TRP D 273 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00260 (15566) covalent geometry : angle 0.55204 (21086) hydrogen bonds : bond 0.04236 ( 718) hydrogen bonds : angle 4.01156 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 240 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5173 (OUTLIER) cc_final: 0.4493 (ptt90) REVERT: A 55 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6182 (m170) REVERT: A 151 ARG cc_start: 0.7003 (tpp80) cc_final: 0.5411 (mtm180) REVERT: A 155 GLN cc_start: 0.6875 (mm-40) cc_final: 0.6555 (tp-100) REVERT: A 168 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 233 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7000 (pp20) REVERT: A 321 ARG cc_start: 0.7475 (mmm160) cc_final: 0.7272 (mmm160) REVERT: A 331 CYS cc_start: 0.7730 (m) cc_final: 0.6990 (p) REVERT: A 343 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5433 (tp40) REVERT: A 431 ARG cc_start: 0.8153 (ptm-80) cc_final: 0.7897 (ptm-80) REVERT: B 209 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6452 (pt0) REVERT: B 257 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7964 (t70) REVERT: B 319 TYR cc_start: 0.8191 (t80) cc_final: 0.7933 (t80) REVERT: B 339 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6115 (ttm110) REVERT: B 360 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: B 394 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 403 GLU cc_start: 0.6789 (pt0) cc_final: 0.6071 (pm20) REVERT: B 418 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6455 (mt) REVERT: B 423 GLN cc_start: 0.6422 (pm20) cc_final: 0.6166 (pm20) REVERT: B 461 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6151 (pp20) REVERT: B 484 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6520 (mm-40) REVERT: B 512 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.6569 (t0) REVERT: C 47 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4500 (ptt90) REVERT: C 55 HIS cc_start: 0.6773 (OUTLIER) cc_final: 0.6497 (m170) REVERT: C 106 MET cc_start: 0.6394 (ttp) cc_final: 0.6189 (tmm) REVERT: C 151 ARG cc_start: 0.7051 (tpp80) cc_final: 0.6568 (mmt90) REVERT: C 155 GLN cc_start: 0.6693 (mm-40) cc_final: 0.6378 (tp-100) REVERT: C 187 PHE cc_start: 0.7081 (t80) cc_final: 0.6828 (t80) REVERT: C 188 TRP cc_start: 0.7785 (m100) cc_final: 0.7515 (m100) REVERT: C 190 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7797 (ttt90) REVERT: C 233 GLU cc_start: 0.7557 (pm20) cc_final: 0.7224 (pp20) REVERT: C 321 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7369 (mmm160) REVERT: C 331 CYS cc_start: 0.7720 (m) cc_final: 0.6822 (p) REVERT: C 343 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5619 (tp40) REVERT: C 387 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: C 392 TYR cc_start: 0.8101 (m-80) cc_final: 0.7792 (m-80) REVERT: C 429 ILE cc_start: 0.7329 (mp) cc_final: 0.7102 (tt) REVERT: D 209 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6287 (pt0) REVERT: D 257 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7896 (t70) REVERT: D 280 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8661 (mmm) REVERT: D 319 TYR cc_start: 0.8247 (t80) cc_final: 0.7761 (t80) REVERT: D 334 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5695 (mmp-170) REVERT: D 338 MET cc_start: 0.6258 (tpp) cc_final: 0.5996 (tpt) REVERT: D 367 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6936 (mm110) REVERT: D 394 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: D 403 GLU cc_start: 0.6772 (pt0) cc_final: 0.6056 (pm20) REVERT: D 418 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6392 (mt) REVERT: D 461 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6256 (pp20) REVERT: D 484 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6266 (mm-40) REVERT: D 512 ASN cc_start: 0.6708 (m-40) cc_final: 0.6437 (t0) REVERT: D 519 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6203 (pp) outliers start: 113 outliers final: 33 residues processed: 323 average time/residue: 0.5631 time to fit residues: 200.3463 Evaluate side-chains 278 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 343 GLN 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 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 257 ASP 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 415 LEU Chi-restraints excluded: chain B residue 418 LEU 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 512 ASN 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 71 THR Chi-restraints excluded: chain C residue 235 SER 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 108 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 486 ASN B 219 HIS C 342 GLN C 487 ASN D 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.205928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137350 restraints weight = 16425.646| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.14 r_work: 0.3333 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15566 Z= 0.241 Angle : 0.652 8.109 21086 Z= 0.345 Chirality : 0.047 0.175 2370 Planarity : 0.005 0.044 2622 Dihedral : 10.482 86.845 2213 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 7.64 % Allowed : 29.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 1836 helix: -0.46 (0.16), residues: 1076 sheet: -0.58 (0.46), residues: 106 loop : -1.89 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 374 TYR 0.016 0.002 TYR C 57 PHE 0.029 0.002 PHE B 110 TRP 0.016 0.003 TRP D 273 HIS 0.009 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00583 (15566) covalent geometry : angle 0.65216 (21086) hydrogen bonds : bond 0.05372 ( 718) hydrogen bonds : angle 4.23296 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 240 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.4492 (ptt90) REVERT: A 55 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6224 (m170) REVERT: A 106 MET cc_start: 0.6381 (ttp) cc_final: 0.6162 (tmm) REVERT: A 151 ARG cc_start: 0.6956 (tpp80) cc_final: 0.5303 (mtm180) REVERT: A 168 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 182 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.6028 (mpp80) REVERT: A 233 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7007 (pp20) REVERT: A 321 ARG cc_start: 0.7510 (mmm160) cc_final: 0.7200 (mmm160) REVERT: A 331 CYS cc_start: 0.7786 (m) cc_final: 0.6996 (p) REVERT: A 335 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6047 (mpt-90) REVERT: B 140 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7731 (p) REVERT: B 195 PHE cc_start: 0.8867 (m-80) cc_final: 0.8590 (m-80) REVERT: B 197 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8049 (p0) REVERT: B 209 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6212 (pt0) REVERT: B 257 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7974 (t70) REVERT: B 319 TYR cc_start: 0.8111 (t80) cc_final: 0.7872 (t80) REVERT: B 339 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6113 (ttm110) REVERT: B 360 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: B 394 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: B 403 GLU cc_start: 0.6694 (pt0) cc_final: 0.5931 (pm20) REVERT: B 418 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6197 (mt) REVERT: B 423 GLN cc_start: 0.6388 (pm20) cc_final: 0.6175 (pm20) REVERT: B 461 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6216 (pp20) REVERT: B 484 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6434 (mm110) REVERT: B 519 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6126 (pp) REVERT: C 47 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4486 (ptt90) REVERT: C 55 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.6584 (m170) REVERT: C 151 ARG cc_start: 0.7021 (tpp80) cc_final: 0.5466 (mtm180) REVERT: C 155 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6608 (tp-100) REVERT: C 168 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7507 (mp) REVERT: C 182 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.5976 (mpp80) REVERT: C 187 PHE cc_start: 0.7054 (t80) cc_final: 0.6816 (t80) REVERT: C 188 TRP cc_start: 0.7615 (m100) cc_final: 0.7323 (m100) REVERT: C 233 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6998 (pp20) REVERT: C 331 CYS cc_start: 0.7781 (m) cc_final: 0.7049 (p) REVERT: C 347 LEU cc_start: 0.6615 (mm) cc_final: 0.6390 (mm) REVERT: C 387 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: C 392 TYR cc_start: 0.8096 (m-80) cc_final: 0.7855 (m-80) REVERT: D 140 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7714 (p) REVERT: D 197 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8030 (p0) REVERT: D 209 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6199 (pt0) REVERT: D 257 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7913 (t70) REVERT: D 280 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8550 (mmp) REVERT: D 319 TYR cc_start: 0.8123 (t80) cc_final: 0.7789 (t80) REVERT: D 334 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5663 (mmp-170) REVERT: D 338 MET cc_start: 0.6271 (tpp) cc_final: 0.6026 (tpt) REVERT: D 362 MET cc_start: 0.7701 (mtp) cc_final: 0.7379 (mtm) REVERT: D 367 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6695 (mm110) REVERT: D 394 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: D 403 GLU cc_start: 0.6623 (pt0) cc_final: 0.5896 (pm20) REVERT: D 484 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6509 (tp-100) REVERT: D 519 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6228 (pp) outliers start: 125 outliers final: 54 residues processed: 336 average time/residue: 0.5130 time to fit residues: 190.8850 Evaluate side-chains 305 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 147 GLU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 405 TYR 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 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 168 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 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 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 140 SER 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 280 MET Chi-restraints excluded: chain D residue 284 ILE 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 405 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.210152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143651 restraints weight = 16452.723| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.23 r_work: 0.3345 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15566 Z= 0.116 Angle : 0.543 8.769 21086 Z= 0.284 Chirality : 0.042 0.147 2370 Planarity : 0.004 0.039 2622 Dihedral : 9.530 81.728 2211 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 6.60 % Allowed : 31.36 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1836 helix: 0.10 (0.16), residues: 1064 sheet: -0.71 (0.45), residues: 116 loop : -1.82 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.012 0.001 TYR D 319 PHE 0.018 0.001 PHE A 361 TRP 0.009 0.001 TRP B 273 HIS 0.007 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00259 (15566) covalent geometry : angle 0.54332 (21086) hydrogen bonds : bond 0.04013 ( 718) hydrogen bonds : angle 3.83086 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 236 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5102 (OUTLIER) cc_final: 0.4433 (ptt90) REVERT: A 55 HIS cc_start: 0.6642 (OUTLIER) cc_final: 0.6311 (m170) REVERT: A 151 ARG cc_start: 0.6899 (tpp80) cc_final: 0.5330 (mtm180) REVERT: A 162 MET cc_start: 0.8768 (tpt) cc_final: 0.8390 (mmm) REVERT: A 182 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5979 (mpp80) REVERT: A 233 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7058 (pp20) REVERT: A 321 ARG cc_start: 0.7546 (mmm160) cc_final: 0.7265 (mmm160) REVERT: A 331 CYS cc_start: 0.7917 (m) cc_final: 0.7250 (p) REVERT: A 335 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6171 (mpt-90) REVERT: A 343 GLN cc_start: 0.5557 (OUTLIER) cc_final: 0.5349 (tp40) REVERT: A 388 MET cc_start: 0.8264 (ttt) cc_final: 0.8029 (ttp) REVERT: B 197 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8274 (p0) REVERT: B 257 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8057 (t70) REVERT: B 319 TYR cc_start: 0.8337 (t80) cc_final: 0.8111 (t80) REVERT: B 339 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6094 (ttm110) REVERT: B 360 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 394 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: B 403 GLU cc_start: 0.6984 (pt0) cc_final: 0.6397 (pm20) REVERT: B 418 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6411 (mt) REVERT: B 423 GLN cc_start: 0.6247 (pm20) cc_final: 0.5995 (pm20) REVERT: B 461 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6435 (pp20) REVERT: B 484 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6507 (mm-40) REVERT: B 519 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6209 (pp) REVERT: C 47 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4401 (ptt90) REVERT: C 55 HIS cc_start: 0.6698 (OUTLIER) cc_final: 0.6437 (m170) REVERT: C 106 MET cc_start: 0.6269 (ttp) cc_final: 0.6057 (tmm) REVERT: C 151 ARG cc_start: 0.6978 (tpp80) cc_final: 0.5492 (mtm180) REVERT: C 162 MET cc_start: 0.8737 (tpt) cc_final: 0.8283 (mmm) REVERT: C 182 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.6023 (mpp80) REVERT: C 187 PHE cc_start: 0.7189 (t80) cc_final: 0.6913 (t80) REVERT: C 188 TRP cc_start: 0.7712 (m100) cc_final: 0.7417 (m100) REVERT: C 233 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7034 (pp20) REVERT: C 331 CYS cc_start: 0.7926 (m) cc_final: 0.7273 (p) REVERT: C 387 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: C 392 TYR cc_start: 0.8157 (m-80) cc_final: 0.7861 (m-80) REVERT: D 66 PHE cc_start: 0.7867 (t80) cc_final: 0.7615 (t80) REVERT: D 197 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8226 (p0) REVERT: D 209 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6679 (pt0) REVERT: D 257 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8012 (t70) REVERT: D 280 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8703 (mmm) REVERT: D 319 TYR cc_start: 0.8295 (t80) cc_final: 0.7943 (t80) REVERT: D 338 MET cc_start: 0.6418 (tpp) cc_final: 0.6163 (tpt) REVERT: D 362 MET cc_start: 0.7789 (mtp) cc_final: 0.7566 (mtm) REVERT: D 367 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7063 (mm110) REVERT: D 376 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7548 (ptp-170) REVERT: D 394 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: D 403 GLU cc_start: 0.7011 (pt0) cc_final: 0.6434 (pm20) REVERT: D 423 GLN cc_start: 0.6309 (pm20) cc_final: 0.6015 (pm20) REVERT: D 484 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6521 (tp-100) REVERT: D 519 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6348 (pp) outliers start: 108 outliers final: 39 residues processed: 314 average time/residue: 0.5204 time to fit residues: 180.1396 Evaluate side-chains 285 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 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 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 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 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 71 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 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 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 174 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS B 330 HIS B 512 ASN C 342 GLN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.207481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137363 restraints weight = 16358.691| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.10 r_work: 0.3314 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15566 Z= 0.191 Angle : 0.609 8.020 21086 Z= 0.318 Chirality : 0.045 0.168 2370 Planarity : 0.004 0.041 2622 Dihedral : 9.847 85.300 2203 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 6.78 % Allowed : 31.85 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 1836 helix: 0.03 (0.16), residues: 1072 sheet: -0.46 (0.46), residues: 106 loop : -1.87 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.019 0.002 TYR D 405 PHE 0.026 0.002 PHE B 110 TRP 0.013 0.002 TRP D 273 HIS 0.008 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00457 (15566) covalent geometry : angle 0.60911 (21086) hydrogen bonds : bond 0.04782 ( 718) hydrogen bonds : angle 3.94602 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 226 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4394 (ptt90) REVERT: A 55 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.6284 (m170) REVERT: A 151 ARG cc_start: 0.6984 (tpp80) cc_final: 0.5476 (mtm180) REVERT: A 152 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 162 MET cc_start: 0.8627 (tpt) cc_final: 0.8121 (mmm) REVERT: A 182 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5944 (mpp80) REVERT: A 233 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: A 321 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7185 (mmm160) REVERT: A 331 CYS cc_start: 0.7803 (m) cc_final: 0.7112 (p) REVERT: A 335 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6042 (mpt-90) REVERT: B 197 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8048 (p0) REVERT: B 257 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8005 (t70) REVERT: B 319 TYR cc_start: 0.8124 (t80) cc_final: 0.7899 (t80) REVERT: B 339 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6044 (ttm110) REVERT: B 360 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: B 362 MET cc_start: 0.7569 (mtp) cc_final: 0.7290 (mtm) REVERT: B 394 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: B 403 GLU cc_start: 0.6810 (pt0) cc_final: 0.6101 (pm20) REVERT: B 423 GLN cc_start: 0.5670 (pm20) cc_final: 0.5395 (pm20) REVERT: B 432 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6443 (pt0) REVERT: B 435 LEU cc_start: 0.7865 (mt) cc_final: 0.7620 (mm) REVERT: B 484 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6319 (mm110) REVERT: B 519 ILE cc_start: 0.6325 (OUTLIER) cc_final: 0.6047 (pp) REVERT: C 47 ARG cc_start: 0.5191 (OUTLIER) cc_final: 0.4472 (ptt90) REVERT: C 55 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6548 (m170) REVERT: C 106 MET cc_start: 0.6243 (ttp) cc_final: 0.6018 (tmm) REVERT: C 151 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6667 (mmt90) REVERT: C 152 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7441 (tp) REVERT: C 162 MET cc_start: 0.8569 (tpt) cc_final: 0.8063 (mmm) REVERT: C 168 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 182 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5997 (mpp80) REVERT: C 187 PHE cc_start: 0.7049 (t80) cc_final: 0.6787 (t80) REVERT: C 188 TRP cc_start: 0.7571 (m100) cc_final: 0.7288 (m100) REVERT: C 233 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: C 331 CYS cc_start: 0.7751 (m) cc_final: 0.7070 (p) REVERT: C 374 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7403 (ptp90) REVERT: C 387 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: C 392 TYR cc_start: 0.8063 (m-80) cc_final: 0.7798 (m-80) REVERT: D 197 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8024 (p0) REVERT: D 209 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6430 (pt0) REVERT: D 257 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8006 (t70) REVERT: D 280 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8751 (mmp) REVERT: D 319 TYR cc_start: 0.8116 (t80) cc_final: 0.7772 (t80) REVERT: D 338 MET cc_start: 0.6276 (tpp) cc_final: 0.6031 (tpt) REVERT: D 362 MET cc_start: 0.7563 (mtp) cc_final: 0.7332 (mtm) REVERT: D 367 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6756 (mm110) REVERT: D 376 ARG cc_start: 0.7659 (ptp-170) cc_final: 0.7303 (ptp-170) REVERT: D 394 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: D 403 GLU cc_start: 0.6884 (pt0) cc_final: 0.6235 (pm20) REVERT: D 423 GLN cc_start: 0.6155 (pm20) cc_final: 0.5824 (pm20) REVERT: D 484 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.6305 (mm110) REVERT: D 519 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6311 (pp) outliers start: 111 outliers final: 50 residues processed: 316 average time/residue: 0.5345 time to fit residues: 185.9537 Evaluate side-chains 296 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 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 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 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain B residue 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 71 THR Chi-restraints excluded: chain C residue 152 ILE 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 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 374 ARG 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 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 280 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 396 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.0030 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.211996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147491 restraints weight = 16272.581| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.15 r_work: 0.3393 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15566 Z= 0.102 Angle : 0.526 7.903 21086 Z= 0.272 Chirality : 0.041 0.142 2370 Planarity : 0.004 0.050 2622 Dihedral : 8.900 78.907 2203 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 5.62 % Allowed : 32.27 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1836 helix: 0.33 (0.16), residues: 1086 sheet: -0.73 (0.45), residues: 116 loop : -1.76 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 321 TYR 0.012 0.001 TYR A 283 PHE 0.015 0.001 PHE A 361 TRP 0.012 0.001 TRP B 237 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00221 (15566) covalent geometry : angle 0.52614 (21086) hydrogen bonds : bond 0.03648 ( 718) hydrogen bonds : angle 3.65213 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 244 time to evaluate : 0.612 Fit side-chains REVERT: A 47 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4469 (ptt90) REVERT: A 55 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6546 (m170) REVERT: A 151 ARG cc_start: 0.6966 (tpp80) cc_final: 0.5456 (mtm180) REVERT: A 152 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7466 (tp) REVERT: A 155 GLN cc_start: 0.7716 (pm20) cc_final: 0.7498 (pm20) REVERT: A 162 MET cc_start: 0.8817 (tpt) cc_final: 0.8364 (mmm) REVERT: A 182 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.6032 (mpp80) REVERT: A 233 GLU cc_start: 0.7462 (pm20) cc_final: 0.6977 (pp20) REVERT: A 321 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7327 (mmm160) REVERT: A 331 CYS cc_start: 0.7928 (m) cc_final: 0.7364 (p) REVERT: A 335 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6187 (mpp80) REVERT: A 367 MET cc_start: 0.7520 (tpt) cc_final: 0.7250 (tpp) REVERT: A 411 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.7029 (pt) REVERT: B 66 PHE cc_start: 0.7833 (t80) cc_final: 0.7628 (t80) REVERT: B 168 MET cc_start: 0.7554 (mmt) cc_final: 0.7262 (mmm) REVERT: B 319 TYR cc_start: 0.8350 (t80) cc_final: 0.8101 (t80) REVERT: B 330 HIS cc_start: 0.7206 (m170) cc_final: 0.6510 (t70) REVERT: B 360 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: B 394 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: B 403 GLU cc_start: 0.7153 (pt0) cc_final: 0.6627 (pm20) REVERT: B 484 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6452 (mm-40) REVERT: B 519 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6294 (pp) REVERT: C 47 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4439 (ptt90) REVERT: C 55 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.6305 (m170) REVERT: C 106 MET cc_start: 0.6532 (ttp) cc_final: 0.6309 (tmm) REVERT: C 151 ARG cc_start: 0.7000 (tpp80) cc_final: 0.6589 (mmt90) REVERT: C 152 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7546 (tp) REVERT: C 162 MET cc_start: 0.8760 (tpt) cc_final: 0.8313 (mmm) REVERT: C 187 PHE cc_start: 0.7276 (t80) cc_final: 0.6974 (t80) REVERT: C 188 TRP cc_start: 0.7765 (m100) cc_final: 0.7493 (m100) REVERT: C 233 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: C 248 ILE cc_start: 0.8823 (mm) cc_final: 0.8588 (mm) REVERT: C 331 CYS cc_start: 0.7949 (m) cc_final: 0.7420 (p) REVERT: C 387 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: C 392 TYR cc_start: 0.8147 (m-80) cc_final: 0.7642 (m-80) REVERT: C 393 PHE cc_start: 0.8485 (m-80) cc_final: 0.8233 (m-80) REVERT: D 167 VAL cc_start: 0.7996 (p) cc_final: 0.7732 (m) REVERT: D 168 MET cc_start: 0.7551 (mmt) cc_final: 0.7245 (mmm) REVERT: D 189 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7257 (mtt90) REVERT: D 280 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8515 (mmp) REVERT: D 319 TYR cc_start: 0.8365 (t80) cc_final: 0.7971 (t80) REVERT: D 338 MET cc_start: 0.6485 (tpp) cc_final: 0.6218 (tpt) REVERT: D 362 MET cc_start: 0.7696 (mtp) cc_final: 0.7463 (mtm) REVERT: D 394 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: D 403 GLU cc_start: 0.7212 (pt0) cc_final: 0.6704 (pm20) REVERT: D 421 GLN cc_start: 0.7874 (mp10) cc_final: 0.7418 (mp10) REVERT: D 423 GLN cc_start: 0.6067 (pm20) cc_final: 0.5758 (pm20) REVERT: D 484 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6475 (mm110) REVERT: D 492 ARG cc_start: 0.6660 (ttm-80) cc_final: 0.6202 (mtm180) REVERT: D 519 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6406 (pp) outliers start: 92 outliers final: 30 residues processed: 316 average time/residue: 0.5967 time to fit residues: 207.3194 Evaluate side-chains 267 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLN Chi-restraints excluded: chain 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 65 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 345 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 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 86 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 487 ASN D 219 HIS D 367 GLN D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.208095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140074 restraints weight = 16515.049| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.09 r_work: 0.3362 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15566 Z= 0.153 Angle : 0.576 8.604 21086 Z= 0.297 Chirality : 0.044 0.224 2370 Planarity : 0.004 0.052 2622 Dihedral : 8.945 82.266 2196 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 5.32 % Allowed : 33.56 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1836 helix: 0.33 (0.16), residues: 1076 sheet: -0.85 (0.44), residues: 116 loop : -1.76 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.020 0.002 TYR D 405 PHE 0.021 0.002 PHE D 110 TRP 0.011 0.002 TRP D 273 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00363 (15566) covalent geometry : angle 0.57629 (21086) hydrogen bonds : bond 0.04364 ( 718) hydrogen bonds : angle 3.76694 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 0.657 Fit side-chains REVERT: A 47 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4388 (ptt90) REVERT: A 55 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6476 (m170) REVERT: A 151 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6694 (mmt90) REVERT: A 152 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 162 MET cc_start: 0.8668 (tpt) cc_final: 0.8194 (mmm) REVERT: A 182 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5964 (mpp80) REVERT: A 233 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: A 321 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7213 (mmm160) REVERT: A 331 CYS cc_start: 0.7815 (m) cc_final: 0.7200 (p) REVERT: A 335 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6064 (mpt-90) REVERT: B 168 MET cc_start: 0.7426 (mmt) cc_final: 0.7113 (mmm) REVERT: B 197 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8117 (p0) REVERT: B 237 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.7262 (t60) REVERT: B 319 TYR cc_start: 0.8177 (t80) cc_final: 0.7828 (t80) REVERT: B 326 ASN cc_start: 0.7737 (t0) cc_final: 0.7478 (t0) REVERT: B 330 HIS cc_start: 0.7218 (m170) cc_final: 0.6521 (t70) REVERT: B 360 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: B 394 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: B 403 GLU cc_start: 0.7141 (pt0) cc_final: 0.6534 (pm20) REVERT: B 484 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6494 (mm110) REVERT: B 519 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6254 (pp) REVERT: C 47 ARG cc_start: 0.5319 (OUTLIER) cc_final: 0.4633 (ptt90) REVERT: C 55 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6516 (m170) REVERT: C 106 MET cc_start: 0.6367 (ttp) cc_final: 0.6106 (tmm) REVERT: C 151 ARG cc_start: 0.7040 (tpp80) cc_final: 0.6627 (mmt90) REVERT: C 152 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7575 (tp) REVERT: C 162 MET cc_start: 0.8647 (tpt) cc_final: 0.8177 (mmm) REVERT: C 182 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.6014 (mpp80) REVERT: C 187 PHE cc_start: 0.7113 (t80) cc_final: 0.6826 (t80) REVERT: C 188 TRP cc_start: 0.7675 (m100) cc_final: 0.7432 (m100) REVERT: C 233 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: C 331 CYS cc_start: 0.7806 (m) cc_final: 0.7178 (p) REVERT: C 392 TYR cc_start: 0.8102 (m-80) cc_final: 0.7763 (m-80) REVERT: C 393 PHE cc_start: 0.8379 (m-80) cc_final: 0.8163 (m-80) REVERT: D 168 MET cc_start: 0.7401 (mmt) cc_final: 0.7096 (mmm) REVERT: D 189 ARG cc_start: 0.7426 (mtt90) cc_final: 0.7214 (mtt90) REVERT: D 197 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (p0) REVERT: D 237 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7255 (t60) REVERT: D 280 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8749 (mmp) REVERT: D 319 TYR cc_start: 0.8248 (t80) cc_final: 0.7809 (t80) REVERT: D 326 ASN cc_start: 0.7563 (t0) cc_final: 0.7195 (t0) REVERT: D 362 MET cc_start: 0.7537 (mtp) cc_final: 0.7286 (mtm) REVERT: D 394 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 403 GLU cc_start: 0.7143 (pt0) cc_final: 0.6634 (pm20) REVERT: D 421 GLN cc_start: 0.7764 (mp10) cc_final: 0.7286 (mp10) REVERT: D 423 GLN cc_start: 0.6030 (pm20) cc_final: 0.5681 (pm20) REVERT: D 484 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6508 (mm110) REVERT: D 519 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6344 (pp) outliers start: 87 outliers final: 38 residues processed: 283 average time/residue: 0.5794 time to fit residues: 180.8690 Evaluate side-chains 273 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG 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 299 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 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 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 350 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 459 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 152 ILE 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 305 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 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 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 145 optimal weight: 0.0050 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 487 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.211891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145895 restraints weight = 16432.744| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.04 r_work: 0.3421 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15566 Z= 0.100 Angle : 0.536 9.109 21086 Z= 0.272 Chirality : 0.041 0.184 2370 Planarity : 0.004 0.055 2622 Dihedral : 8.257 76.118 2196 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.65 % Allowed : 34.11 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1836 helix: 0.50 (0.16), residues: 1098 sheet: -0.66 (0.45), residues: 116 loop : -1.72 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.011 0.001 TYR A 283 PHE 0.019 0.001 PHE B 66 TRP 0.015 0.001 TRP A 188 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00217 (15566) covalent geometry : angle 0.53564 (21086) hydrogen bonds : bond 0.03586 ( 718) hydrogen bonds : angle 3.58616 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.4363 (ptt90) REVERT: A 55 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.6507 (m170) REVERT: A 151 ARG cc_start: 0.6921 (tpp80) cc_final: 0.5402 (mtm180) REVERT: A 152 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7335 (tp) REVERT: A 162 MET cc_start: 0.8688 (tpt) cc_final: 0.8219 (mmm) REVERT: A 182 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.6016 (mpp80) REVERT: A 233 GLU cc_start: 0.7126 (pm20) cc_final: 0.6874 (pm20) REVERT: A 321 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7269 (mmm160) REVERT: A 331 CYS cc_start: 0.7761 (m) cc_final: 0.7239 (p) REVERT: A 335 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6209 (mpt180) REVERT: A 343 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.5762 (tt0) REVERT: A 387 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: A 466 ASN cc_start: 0.6825 (m-40) cc_final: 0.6622 (t0) REVERT: B 68 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6037 (tp30) REVERT: B 319 TYR cc_start: 0.8197 (t80) cc_final: 0.7821 (t80) REVERT: B 330 HIS cc_start: 0.7179 (m170) cc_final: 0.6623 (t70) REVERT: B 360 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: B 394 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: B 403 GLU cc_start: 0.7109 (pt0) cc_final: 0.6601 (pm20) REVERT: B 426 TYR cc_start: 0.7746 (m-80) cc_final: 0.7282 (m-80) REVERT: B 484 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6276 (mm-40) REVERT: B 519 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6265 (pp) REVERT: C 47 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.4747 (ptt90) REVERT: C 106 MET cc_start: 0.6343 (ttp) cc_final: 0.6105 (tmm) REVERT: C 151 ARG cc_start: 0.6993 (tpp80) cc_final: 0.6569 (mmt90) REVERT: C 152 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7473 (tp) REVERT: C 162 MET cc_start: 0.8651 (tpt) cc_final: 0.8188 (mmm) REVERT: C 182 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.6105 (mpp80) REVERT: C 187 PHE cc_start: 0.7169 (t80) cc_final: 0.6847 (t80) REVERT: C 188 TRP cc_start: 0.7647 (m100) cc_final: 0.7340 (m100) REVERT: C 233 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: C 331 CYS cc_start: 0.7756 (m) cc_final: 0.7254 (p) REVERT: C 392 TYR cc_start: 0.8073 (m-80) cc_final: 0.7489 (m-80) REVERT: C 466 ASN cc_start: 0.6832 (m-40) cc_final: 0.6611 (t0) REVERT: D 167 VAL cc_start: 0.7841 (p) cc_final: 0.7601 (m) REVERT: D 319 TYR cc_start: 0.8231 (t80) cc_final: 0.7675 (t80) REVERT: D 362 MET cc_start: 0.7644 (mtp) cc_final: 0.7383 (mtm) REVERT: D 394 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: D 403 GLU cc_start: 0.7041 (pt0) cc_final: 0.6554 (pm20) REVERT: D 418 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6315 (mt) REVERT: D 421 GLN cc_start: 0.7745 (mp10) cc_final: 0.7260 (mp10) REVERT: D 423 GLN cc_start: 0.5870 (pm20) cc_final: 0.5534 (pm20) REVERT: D 461 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7002 (pt0) REVERT: D 484 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6300 (mm-40) REVERT: D 492 ARG cc_start: 0.6399 (ttm-80) cc_final: 0.5997 (mtm180) REVERT: D 519 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6346 (pp) outliers start: 76 outliers final: 29 residues processed: 288 average time/residue: 0.6163 time to fit residues: 195.3023 Evaluate side-chains 261 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 345 ILE 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 441 THR Chi-restraints excluded: chain B residue 459 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 65 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 152 ILE 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 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 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 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 176 optimal weight: 0.0030 chunk 38 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 219 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 487 ASN D 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.212649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144738 restraints weight = 16315.397| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.88 r_work: 0.3381 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15566 Z= 0.106 Angle : 0.548 9.441 21086 Z= 0.280 Chirality : 0.042 0.194 2370 Planarity : 0.004 0.064 2622 Dihedral : 7.818 75.545 2190 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.67 % Allowed : 34.96 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1836 helix: 0.58 (0.16), residues: 1102 sheet: -0.74 (0.44), residues: 116 loop : -1.64 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 321 TYR 0.021 0.001 TYR D 405 PHE 0.027 0.001 PHE B 486 TRP 0.023 0.001 TRP A 188 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00238 (15566) covalent geometry : angle 0.54775 (21086) hydrogen bonds : bond 0.03666 ( 718) hydrogen bonds : angle 3.54863 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5082 (OUTLIER) cc_final: 0.4354 (ptt90) REVERT: A 55 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6457 (m170) REVERT: A 151 ARG cc_start: 0.6919 (tpp80) cc_final: 0.6511 (mmt90) REVERT: A 152 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7404 (tp) REVERT: A 162 MET cc_start: 0.8575 (tpt) cc_final: 0.8047 (mmm) REVERT: A 182 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5993 (mpp80) REVERT: A 233 GLU cc_start: 0.7241 (pm20) cc_final: 0.6903 (pm20) REVERT: A 321 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7229 (mmm160) REVERT: A 331 CYS cc_start: 0.7696 (m) cc_final: 0.7162 (p) REVERT: A 335 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6117 (mpt180) REVERT: A 343 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5733 (tt0) REVERT: A 466 ASN cc_start: 0.6723 (m-40) cc_final: 0.6497 (t0) REVERT: B 237 TRP cc_start: 0.8273 (OUTLIER) cc_final: 0.7223 (t60) REVERT: B 319 TYR cc_start: 0.8112 (t80) cc_final: 0.7695 (t80) REVERT: B 330 HIS cc_start: 0.7083 (m170) cc_final: 0.6594 (t70) REVERT: B 360 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: B 362 MET cc_start: 0.7419 (mtp) cc_final: 0.7210 (mtm) REVERT: B 394 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7411 (tm130) REVERT: B 403 GLU cc_start: 0.7037 (pt0) cc_final: 0.6466 (pm20) REVERT: B 426 TYR cc_start: 0.7703 (m-80) cc_final: 0.7151 (m-80) REVERT: C 47 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.4554 (mmp-170) REVERT: C 151 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6527 (mmt90) REVERT: C 152 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7471 (tp) REVERT: C 162 MET cc_start: 0.8603 (tpt) cc_final: 0.8105 (mmm) REVERT: C 182 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.6055 (mpp80) REVERT: C 187 PHE cc_start: 0.6966 (t80) cc_final: 0.6646 (t80) REVERT: C 188 TRP cc_start: 0.7602 (m100) cc_final: 0.7304 (m100) REVERT: C 233 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6664 (pp20) REVERT: C 331 CYS cc_start: 0.7675 (m) cc_final: 0.7155 (p) REVERT: C 392 TYR cc_start: 0.8054 (m-80) cc_final: 0.7504 (m-80) REVERT: C 466 ASN cc_start: 0.6681 (m-40) cc_final: 0.6463 (t0) REVERT: D 167 VAL cc_start: 0.7766 (p) cc_final: 0.7537 (m) REVERT: D 319 TYR cc_start: 0.8126 (t80) cc_final: 0.7534 (t80) REVERT: D 338 MET cc_start: 0.6136 (tpt) cc_final: 0.5832 (tpt) REVERT: D 362 MET cc_start: 0.7468 (mtp) cc_final: 0.7187 (mtm) REVERT: D 394 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: D 403 GLU cc_start: 0.6930 (pt0) cc_final: 0.6438 (pm20) REVERT: D 418 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6310 (mt) REVERT: D 421 GLN cc_start: 0.7678 (mp10) cc_final: 0.7192 (mp10) REVERT: D 423 GLN cc_start: 0.5779 (pm20) cc_final: 0.5507 (pm20) REVERT: D 461 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7005 (pt0) REVERT: D 492 ARG cc_start: 0.6312 (ttm-80) cc_final: 0.5893 (mtm180) outliers start: 60 outliers final: 26 residues processed: 262 average time/residue: 0.5946 time to fit residues: 171.6469 Evaluate side-chains 254 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 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 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 152 ILE 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 381 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 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 415 LEU Chi-restraints excluded: chain D residue 418 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 522 ASN D 512 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146336 restraints weight = 16356.015| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.12 r_work: 0.3416 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15566 Z= 0.114 Angle : 0.555 8.890 21086 Z= 0.283 Chirality : 0.042 0.183 2370 Planarity : 0.004 0.072 2622 Dihedral : 7.686 76.528 2190 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 3.12 % Allowed : 35.76 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1836 helix: 0.63 (0.16), residues: 1102 sheet: -0.47 (0.47), residues: 102 loop : -1.62 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 321 TYR 0.010 0.001 TYR A 53 PHE 0.027 0.001 PHE B 66 TRP 0.025 0.001 TRP A 188 HIS 0.006 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00261 (15566) covalent geometry : angle 0.55534 (21086) hydrogen bonds : bond 0.03773 ( 718) hydrogen bonds : angle 3.54885 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7134.91 seconds wall clock time: 121 minutes 49.94 seconds (7309.94 seconds total)