Starting phenix.real_space_refine on Sun Jul 21 21:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2024/7wm2_32598.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.159 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 92 5.16 5 C 10072 2.51 5 N 2596 2.21 5 O 2718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D GLU 441": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15485 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3837 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain: "B" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3826 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain: "C" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3837 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain: "D" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3826 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} 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: 8.04, per 1000 atoms: 0.52 Number of scatterers: 15485 At special positions: 0 Unit cell: (117.426, 115.271, 131.431, 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 92 16.00 P 4 15.00 O 2718 8.00 N 2596 7.00 C 10072 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 - 3.50 Amino acid : False - 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: 5.87 Conformation dependent library (CDL) restraints added in 2.6 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 11 sheets defined 67.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 54 through 82 removed outlier: 3.605A pdb=" N ARG A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.803A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.505A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.534A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.674A pdb=" N ALA A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.983A pdb=" N ARG A 164 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.711A pdb=" N LYS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 191 through 216 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.549A pdb=" N LYS A 221 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.645A pdb=" N GLU A 234 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 263 through 316 removed outlier: 3.548A pdb=" N PHE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 298 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 338 removed outlier: 3.502A pdb=" N ASP A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.029A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.591A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.611A pdb=" N VAL A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.823A pdb=" N ILE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.587A pdb=" N GLY A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 removed outlier: 4.493A pdb=" N LEU A 504 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.696A pdb=" N ALA A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 82 removed outlier: 3.827A pdb=" N TRP B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 86 through 95 removed outlier: 4.972A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 removed outlier: 3.811A pdb=" N ALA B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 4.136A pdb=" N PHE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.822A pdb=" N ALA B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.962A pdb=" N ARG B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.537A pdb=" N GLY B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 215 removed outlier: 3.510A pdb=" N HIS B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.686A pdb=" N LYS B 221 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.790A pdb=" N GLU B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 253 Processing helix chain 'B' and resid 263 through 294 Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.845A pdb=" N ASN B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 346 removed outlier: 3.542A pdb=" N ASP B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.737A pdb=" N SER B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.902A pdb=" N ASP B 368 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 369 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.512A pdb=" N LEU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.628A pdb=" N ILE B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.576A pdb=" N ILE B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.932A pdb=" N LEU B 504 " --> pdb=" O MET B 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.560A pdb=" N ILE C 59 " --> pdb=" O HIS C 55 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 63 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 106 removed outlier: 5.033A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.571A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 removed outlier: 3.516A pdb=" N ASP C 139 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.629A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.176A pdb=" N ARG C 164 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.354A pdb=" N LYS C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 216 removed outlier: 3.851A pdb=" N LEU C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.529A pdb=" N LYS C 221 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.770A pdb=" N GLU C 234 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 252 removed outlier: 3.602A pdb=" N ILE C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 296 removed outlier: 3.574A pdb=" N PHE C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.799A pdb=" N ASP C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 removed outlier: 3.722A pdb=" N GLN C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 327 " --> pdb=" O GLN C 323 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.051A pdb=" N LEU C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 368 removed outlier: 4.161A pdb=" N SER C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 358 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 removed outlier: 3.919A pdb=" N LEU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 467 through 475 removed outlier: 4.011A pdb=" N ILE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 3.741A pdb=" N THR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.789A pdb=" N LEU C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 82 removed outlier: 3.603A pdb=" N ALA D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 86 through 95 removed outlier: 4.816A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.797A pdb=" N ALA D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 removed outlier: 4.177A pdb=" N PHE D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.762A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.930A pdb=" N ARG D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 185 through 215 removed outlier: 3.807A pdb=" N ALA D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.779A pdb=" N LYS D 221 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 263 through 294 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.589A pdb=" N ASP D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 306 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 349 removed outlier: 3.525A pdb=" N GLN D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 4.869A pdb=" N SER D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.745A pdb=" N ARG D 374 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.590A pdb=" N PHE D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 447 removed outlier: 4.004A pdb=" N VAL D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 475 removed outlier: 3.556A pdb=" N ILE D 474 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 495 removed outlier: 3.503A pdb=" N ASN D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 4.022A pdb=" N VAL D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.790A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 433 removed outlier: 4.864A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 393 removed outlier: 7.121A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 439 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 393 removed outlier: 7.121A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 400 removed outlier: 6.907A pdb=" N ASP B 398 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 456 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 400 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 431 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.869A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 410 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 426 through 433 removed outlier: 3.501A pdb=" N ASP C 423 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU C 419 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU C 432 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA C 417 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 393 removed outlier: 7.054A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 439 " --> pdb=" O TYR D 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 398 through 400 removed outlier: 7.026A pdb=" N ASP D 398 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR D 456 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 400 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2394 1.27 - 1.40: 4238 1.40 - 1.54: 8969 1.54 - 1.67: 89 1.67 - 1.81: 156 Bond restraints: 15846 Sorted by residual: bond pdb=" C PRO C 76 " pdb=" O PRO C 76 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.26e-02 6.30e+03 7.09e+01 bond pdb=" C PRO A 76 " pdb=" O PRO A 76 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.26e-02 6.30e+03 6.87e+01 bond pdb=" C PRO D 76 " pdb=" O PRO D 76 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.26e-02 6.30e+03 6.82e+01 bond pdb=" C PRO B 76 " pdb=" O PRO B 76 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.26e-02 6.30e+03 6.69e+01 bond pdb=" C THR A 250 " pdb=" O THR A 250 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.19e-02 7.06e+03 6.46e+01 ... (remaining 15841 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.91: 282 104.91 - 112.59: 8248 112.59 - 120.26: 6976 120.26 - 127.94: 5827 127.94 - 135.61: 143 Bond angle restraints: 21476 Sorted by residual: angle pdb=" N GLN A 344 " pdb=" CA GLN A 344 " pdb=" C GLN A 344 " ideal model delta sigma weight residual 114.56 104.96 9.60 1.27e+00 6.20e-01 5.71e+01 angle pdb=" CA THR B 250 " pdb=" CB THR B 250 " pdb=" OG1 THR B 250 " ideal model delta sigma weight residual 109.60 99.30 10.30 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA ARG B 300 " pdb=" C ARG B 300 " pdb=" N ASN B 301 " ideal model delta sigma weight residual 116.92 124.70 -7.78 1.16e+00 7.43e-01 4.50e+01 angle pdb=" N PHE C 187 " pdb=" CA PHE C 187 " pdb=" C PHE C 187 " ideal model delta sigma weight residual 111.36 104.38 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" C GLU B 339 " pdb=" CA GLU B 339 " pdb=" CB GLU B 339 " ideal model delta sigma weight residual 110.79 100.50 10.29 1.66e+00 3.63e-01 3.84e+01 ... (remaining 21471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7999 17.87 - 35.75: 1055 35.75 - 53.62: 291 53.62 - 71.49: 71 71.49 - 89.37: 24 Dihedral angle restraints: 9440 sinusoidal: 3878 harmonic: 5562 Sorted by residual: dihedral pdb=" C SER B 297 " pdb=" N SER B 297 " pdb=" CA SER B 297 " pdb=" CB SER B 297 " ideal model delta harmonic sigma weight residual -122.60 -138.08 15.48 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" C GLN B 342 " pdb=" N GLN B 342 " pdb=" CA GLN B 342 " pdb=" CB GLN B 342 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" N SER B 297 " pdb=" C SER B 297 " pdb=" CA SER B 297 " pdb=" CB SER B 297 " ideal model delta harmonic sigma weight residual 122.80 136.02 -13.22 0 2.50e+00 1.60e-01 2.80e+01 ... (remaining 9437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2310 0.118 - 0.236: 84 0.236 - 0.354: 19 0.354 - 0.472: 7 0.472 - 0.590: 2 Chirality restraints: 2422 Sorted by residual: chirality pdb=" CA SER B 297 " pdb=" N SER B 297 " pdb=" C SER B 297 " pdb=" CB SER B 297 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" CA GLN B 342 " pdb=" N GLN B 342 " pdb=" C GLN B 342 " pdb=" CB GLN B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CA GLN C 343 " pdb=" N GLN C 343 " pdb=" C GLN C 343 " pdb=" CB GLN C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 2419 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 901 " -0.185 2.00e-02 2.50e+03 1.87e-01 3.49e+02 pdb=" C29 POV B 901 " 0.178 2.00e-02 2.50e+03 pdb="C210 POV B 901 " 0.195 2.00e-02 2.50e+03 pdb="C211 POV B 901 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 901 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C29 POV A 901 " 0.159 2.00e-02 2.50e+03 pdb="C210 POV A 901 " 0.158 2.00e-02 2.50e+03 pdb="C211 POV A 901 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 901 " 0.134 2.00e-02 2.50e+03 1.34e-01 1.81e+02 pdb=" C29 POV C 901 " -0.132 2.00e-02 2.50e+03 pdb="C210 POV C 901 " -0.136 2.00e-02 2.50e+03 pdb="C211 POV C 901 " 0.135 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 1429 2.72 - 3.32: 19247 3.32 - 3.93: 28876 3.93 - 4.53: 40721 4.53 - 5.14: 60142 Nonbonded interactions: 150415 Sorted by model distance: nonbonded pdb=" N ASP B 304 " pdb=" OD1 ASP B 304 " model vdw 2.110 2.520 nonbonded pdb=" O ASN B 301 " pdb=" ND2 ASN B 301 " model vdw 2.171 2.520 nonbonded pdb=" O SER B 356 " pdb=" OG SER B 356 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASP A 139 " pdb=" NE1 TRP A 166 " model vdw 2.209 2.520 nonbonded pdb=" O THR C 252 " pdb=" OG1 THR C 253 " model vdw 2.212 2.440 ... (remaining 150410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 512) selection = (chain 'B' and resid 44 through 512) selection = (chain 'C' and resid 44 through 512) selection = (chain 'D' and resid 44 through 512) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.880 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 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 0.106 15846 Z= 0.755 Angle : 1.035 14.061 21476 Z= 0.640 Chirality : 0.065 0.590 2422 Planarity : 0.008 0.187 2688 Dihedral : 18.172 89.366 5836 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.88 % Favored : 93.96 % Rotamer: Outliers : 12.04 % Allowed : 22.88 % Favored : 65.08 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.16), residues: 1870 helix: -3.02 (0.12), residues: 1096 sheet: -2.76 (0.48), residues: 100 loop : -2.06 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP D 246 HIS 0.020 0.002 HIS B 294 PHE 0.018 0.002 PHE C 184 TYR 0.032 0.002 TYR C 186 ARG 0.012 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 265 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7361 (t70) cc_final: 0.7159 (t0) REVERT: A 124 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6087 (mtt180) REVERT: A 151 ARG cc_start: 0.6571 (ttm170) cc_final: 0.6188 (mtp-110) REVERT: A 159 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 162 MET cc_start: 0.8159 (tpt) cc_final: 0.7761 (tpt) REVERT: A 183 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.5947 (t160) REVERT: A 188 TRP cc_start: 0.6941 (m100) cc_final: 0.6739 (m100) REVERT: A 232 LEU cc_start: 0.8423 (mt) cc_final: 0.8064 (mm) REVERT: A 249 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 267 MET cc_start: 0.8339 (mtt) cc_final: 0.7880 (mtm) REVERT: A 294 HIS cc_start: 0.7319 (m-70) cc_final: 0.7090 (m90) REVERT: A 298 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.7036 (ttm-80) REVERT: A 339 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5502 (mt-10) REVERT: A 343 GLN cc_start: 0.5299 (OUTLIER) cc_final: 0.5032 (mm110) REVERT: A 466 ASN cc_start: 0.5077 (p0) cc_final: 0.4760 (p0) REVERT: A 510 MET cc_start: 0.0472 (mtt) cc_final: -0.0590 (ptm) REVERT: B 46 ARG cc_start: 0.5632 (ttm-80) cc_final: 0.5315 (mtp85) REVERT: B 83 ARG cc_start: 0.7438 (ptp-110) cc_final: 0.7079 (mtm110) REVERT: B 86 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6464 (ptt180) REVERT: B 105 ILE cc_start: 0.7944 (mt) cc_final: 0.7734 (mt) REVERT: B 109 PHE cc_start: 0.7072 (m-10) cc_final: 0.6798 (m-80) REVERT: B 133 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6510 (mtm-85) REVERT: B 162 MET cc_start: 0.8568 (mmt) cc_final: 0.8285 (mmm) REVERT: B 294 HIS cc_start: 0.6670 (m-70) cc_final: 0.6399 (m-70) REVERT: B 301 ASN cc_start: 0.5398 (OUTLIER) cc_final: 0.4709 (p0) REVERT: B 333 LYS cc_start: 0.5701 (tppt) cc_final: 0.5268 (ttpp) REVERT: B 344 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6204 (tm-30) REVERT: B 352 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.4870 (tmtt) REVERT: B 389 LYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4480 (mtmt) REVERT: B 401 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4980 (mt) REVERT: B 485 MET cc_start: 0.4557 (tpt) cc_final: 0.3511 (tpt) REVERT: B 500 MET cc_start: 0.3298 (tmm) cc_final: 0.3051 (ptm) REVERT: C 58 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7318 (mpt-90) REVERT: C 103 ASP cc_start: 0.7696 (t70) cc_final: 0.7352 (t0) REVERT: C 155 GLN cc_start: 0.7742 (mm110) cc_final: 0.7371 (mp10) REVERT: C 177 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6507 (mtp-110) REVERT: C 180 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6055 (pptt) REVERT: C 183 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6059 (t160) REVERT: C 190 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7969 (tpt90) REVERT: C 194 LEU cc_start: 0.7487 (mt) cc_final: 0.7156 (mt) REVERT: C 230 ASN cc_start: 0.6079 (m110) cc_final: 0.5868 (p0) REVERT: C 258 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.6903 (p0) REVERT: C 267 MET cc_start: 0.8327 (mtt) cc_final: 0.7840 (mtm) REVERT: C 288 MET cc_start: 0.7938 (tpt) cc_final: 0.7473 (tpp) REVERT: C 298 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6131 (ttm-80) REVERT: C 314 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.5505 (m-70) REVERT: C 316 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7697 (m110) REVERT: C 343 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.3898 (pp30) REVERT: C 352 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5971 (tppt) REVERT: C 388 MET cc_start: 0.5247 (mtt) cc_final: 0.4929 (mtm) REVERT: C 401 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6275 (pt) REVERT: C 464 ARG cc_start: 0.6100 (ttm170) cc_final: 0.5723 (ttp-110) REVERT: C 504 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6086 (tt) REVERT: D 56 LYS cc_start: 0.6738 (tmtt) cc_final: 0.6196 (mttt) REVERT: D 86 ARG cc_start: 0.6619 (mtp180) cc_final: 0.5942 (ptt180) REVERT: D 93 ASP cc_start: 0.7391 (t0) cc_final: 0.6611 (m-30) REVERT: D 105 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7624 (pp) REVERT: D 109 PHE cc_start: 0.7496 (m-10) cc_final: 0.7258 (m-80) REVERT: D 125 LYS cc_start: 0.7494 (mmtt) cc_final: 0.6669 (pttt) REVERT: D 215 ARG cc_start: 0.6416 (ptt180) cc_final: 0.6210 (mtm110) REVERT: D 294 HIS cc_start: 0.6855 (m-70) cc_final: 0.6523 (m-70) REVERT: D 333 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5398 (tptp) REVERT: D 367 MET cc_start: 0.6166 (tpp) cc_final: 0.5900 (tpt) REVERT: D 398 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5002 (p0) REVERT: D 432 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5205 (pm20) REVERT: D 506 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4362 (pp20) outliers start: 202 outliers final: 65 residues processed: 427 average time/residue: 1.0974 time to fit residues: 520.9758 Evaluate side-chains 307 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 217 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 506 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 294 HIS A 323 GLN A 325 GLN A 383 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 466 ASN A 472 ASN A 502 ASN B 161 ASN B 216 ASN B 218 ASN B 290 ASN B 294 HIS B 472 ASN B 475 GLN C 216 ASN C 323 GLN C 343 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN D 126 GLN D 216 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 383 GLN D 477 ASN D 491 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15846 Z= 0.213 Angle : 0.714 10.492 21476 Z= 0.370 Chirality : 0.045 0.173 2422 Planarity : 0.005 0.036 2688 Dihedral : 12.208 99.971 2384 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 7.51 % Allowed : 26.82 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 1870 helix: -0.97 (0.14), residues: 1146 sheet: -2.25 (0.48), residues: 102 loop : -1.27 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 246 HIS 0.005 0.001 HIS A 360 PHE 0.015 0.001 PHE B 382 TYR 0.020 0.002 TYR D 364 ARG 0.007 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 227 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7358 (t70) cc_final: 0.7086 (t0) REVERT: A 162 MET cc_start: 0.8174 (tpt) cc_final: 0.7730 (tpt) REVERT: A 183 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6018 (t160) REVERT: A 194 LEU cc_start: 0.7662 (mt) cc_final: 0.7377 (mt) REVERT: A 232 LEU cc_start: 0.8511 (mt) cc_final: 0.8251 (mm) REVERT: A 267 MET cc_start: 0.8395 (mtt) cc_final: 0.7962 (mtm) REVERT: A 298 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.7010 (ttm-80) REVERT: A 339 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5649 (mt-10) REVERT: A 432 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7067 (pp20) REVERT: A 464 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5662 (ttp-110) REVERT: A 510 MET cc_start: 0.0230 (mtt) cc_final: -0.0739 (ptm) REVERT: B 83 ARG cc_start: 0.7130 (ptp-110) cc_final: 0.6771 (mtm110) REVERT: B 86 ARG cc_start: 0.6714 (mtp180) cc_final: 0.6032 (ptt180) REVERT: B 93 ASP cc_start: 0.7285 (t0) cc_final: 0.6473 (m-30) REVERT: B 105 ILE cc_start: 0.7799 (mt) cc_final: 0.7563 (mt) REVERT: B 109 PHE cc_start: 0.7038 (m-10) cc_final: 0.6765 (m-80) REVERT: B 133 ARG cc_start: 0.6763 (mtp180) cc_final: 0.6155 (mtm-85) REVERT: B 307 GLN cc_start: 0.7449 (pp30) cc_final: 0.7224 (tp40) REVERT: B 337 ASP cc_start: 0.6710 (m-30) cc_final: 0.6474 (m-30) REVERT: B 352 LYS cc_start: 0.5680 (OUTLIER) cc_final: 0.4440 (tmtt) REVERT: B 397 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6283 (tp30) REVERT: B 401 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4705 (mt) REVERT: B 485 MET cc_start: 0.4415 (tpt) cc_final: 0.3492 (mmt) REVERT: B 495 MET cc_start: 0.5957 (ttm) cc_final: 0.5701 (tpp) REVERT: C 93 ASP cc_start: 0.7842 (t0) cc_final: 0.7506 (m-30) REVERT: C 103 ASP cc_start: 0.7492 (t70) cc_final: 0.7138 (t0) REVERT: C 113 LEU cc_start: 0.7755 (mm) cc_final: 0.7444 (tp) REVERT: C 122 ASP cc_start: 0.6557 (p0) cc_final: 0.6288 (p0) REVERT: C 151 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6911 (ppt170) REVERT: C 155 GLN cc_start: 0.7687 (mm110) cc_final: 0.7278 (mp10) REVERT: C 177 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6596 (ttp-110) REVERT: C 179 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6447 (mm-30) REVERT: C 182 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7072 (mtm-85) REVERT: C 183 ASN cc_start: 0.6824 (m-40) cc_final: 0.6555 (t160) REVERT: C 194 LEU cc_start: 0.7344 (mt) cc_final: 0.7136 (mt) REVERT: C 248 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7882 (mt) REVERT: C 267 MET cc_start: 0.8387 (mtt) cc_final: 0.7923 (mtm) REVERT: C 288 MET cc_start: 0.7836 (tpt) cc_final: 0.7411 (tpp) REVERT: C 298 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6025 (ttm-80) REVERT: C 343 GLN cc_start: 0.5389 (OUTLIER) cc_final: 0.4254 (pp30) REVERT: C 381 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5143 (mp) REVERT: C 388 MET cc_start: 0.4904 (mtt) cc_final: 0.4657 (mtp) REVERT: C 401 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6329 (pp) REVERT: C 441 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.5142 (tt0) REVERT: C 494 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4620 (mp0) REVERT: C 497 ASP cc_start: 0.5609 (OUTLIER) cc_final: 0.5269 (p0) REVERT: D 56 LYS cc_start: 0.6643 (tmtt) cc_final: 0.6155 (mtmm) REVERT: D 86 ARG cc_start: 0.6510 (mtp180) cc_final: 0.5897 (ptt180) REVERT: D 93 ASP cc_start: 0.7214 (t0) cc_final: 0.6478 (m-30) REVERT: D 105 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7788 (pt) REVERT: D 109 PHE cc_start: 0.7375 (m-10) cc_final: 0.7137 (m-80) REVERT: D 125 LYS cc_start: 0.7417 (mmtt) cc_final: 0.6368 (tttt) REVERT: D 162 MET cc_start: 0.8620 (tpt) cc_final: 0.7892 (mmm) REVERT: D 215 ARG cc_start: 0.6486 (ptt180) cc_final: 0.6161 (mtm110) REVERT: D 252 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7047 (t) REVERT: D 294 HIS cc_start: 0.6429 (m-70) cc_final: 0.6114 (m-70) REVERT: D 330 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6332 (mm) REVERT: D 333 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5339 (tptp) REVERT: D 384 LEU cc_start: 0.4191 (OUTLIER) cc_final: 0.3929 (mm) REVERT: D 395 PRO cc_start: 0.7140 (Cg_endo) cc_final: 0.6818 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.4954 (pm20) outliers start: 126 outliers final: 34 residues processed: 330 average time/residue: 1.0687 time to fit residues: 394.7633 Evaluate side-chains 265 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 210 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 218 ASN B 294 HIS B 301 ASN B 343 GLN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 ASN C 472 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 15846 Z= 0.430 Angle : 0.736 10.855 21476 Z= 0.381 Chirality : 0.050 0.334 2422 Planarity : 0.005 0.049 2688 Dihedral : 11.051 106.715 2270 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 8.34 % Allowed : 26.28 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1870 helix: -0.63 (0.14), residues: 1142 sheet: -1.90 (0.51), residues: 100 loop : -1.04 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 246 HIS 0.006 0.002 HIS B 294 PHE 0.022 0.002 PHE D 272 TYR 0.022 0.002 TYR D 245 ARG 0.009 0.001 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 206 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7408 (t70) cc_final: 0.7145 (t0) REVERT: A 125 LYS cc_start: 0.6471 (tppt) cc_final: 0.5915 (ttmm) REVERT: A 162 MET cc_start: 0.8074 (tpt) cc_final: 0.7617 (mmm) REVERT: A 183 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6128 (t160) REVERT: A 267 MET cc_start: 0.8441 (mtt) cc_final: 0.7970 (mtm) REVERT: A 298 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.6974 (ttt90) REVERT: A 339 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5706 (mt-10) REVERT: A 497 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5901 (p0) REVERT: A 510 MET cc_start: 0.0222 (mtt) cc_final: -0.0825 (ptm) REVERT: B 83 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6943 (mtm110) REVERT: B 84 LYS cc_start: 0.7858 (pttm) cc_final: 0.7573 (ptmm) REVERT: B 86 ARG cc_start: 0.6651 (mtp180) cc_final: 0.5934 (ptt180) REVERT: B 93 ASP cc_start: 0.7299 (t0) cc_final: 0.6499 (m-30) REVERT: B 109 PHE cc_start: 0.7054 (m-10) cc_final: 0.6792 (m-80) REVERT: B 133 ARG cc_start: 0.6831 (mtp180) cc_final: 0.6211 (mtm-85) REVERT: B 162 MET cc_start: 0.8666 (tpt) cc_final: 0.7938 (mmm) REVERT: B 238 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6364 (tmt) REVERT: B 248 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7786 (mt) REVERT: B 258 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7269 (p0) REVERT: B 317 HIS cc_start: 0.5570 (OUTLIER) cc_final: 0.4723 (p-80) REVERT: B 337 ASP cc_start: 0.6825 (m-30) cc_final: 0.6573 (m-30) REVERT: B 401 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4381 (mt) REVERT: B 485 MET cc_start: 0.4361 (tpt) cc_final: 0.3477 (mmt) REVERT: B 500 MET cc_start: 0.3917 (ppp) cc_final: 0.3366 (pp-130) REVERT: C 93 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: C 103 ASP cc_start: 0.7517 (t70) cc_final: 0.7138 (t0) REVERT: C 113 LEU cc_start: 0.7649 (mm) cc_final: 0.7381 (tp) REVERT: C 151 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6848 (ppt170) REVERT: C 155 GLN cc_start: 0.7670 (mm110) cc_final: 0.7279 (mp10) REVERT: C 177 ARG cc_start: 0.7093 (mtm110) cc_final: 0.6757 (ttp-110) REVERT: C 179 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6778 (mm-30) REVERT: C 182 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6992 (ttm-80) REVERT: C 183 ASN cc_start: 0.6756 (m-40) cc_final: 0.6357 (t160) REVERT: C 248 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8033 (mt) REVERT: C 267 MET cc_start: 0.8438 (mtt) cc_final: 0.7998 (mtm) REVERT: C 288 MET cc_start: 0.7981 (tpt) cc_final: 0.7476 (tpp) REVERT: C 298 ARG cc_start: 0.6762 (mtp-110) cc_final: 0.6016 (ttm-80) REVERT: C 388 MET cc_start: 0.4679 (mtt) cc_final: 0.4431 (mtp) REVERT: C 392 TYR cc_start: 0.7484 (m-80) cc_final: 0.7235 (m-80) REVERT: C 494 GLU cc_start: 0.4481 (OUTLIER) cc_final: 0.4250 (mp0) REVERT: D 56 LYS cc_start: 0.6771 (tmtt) cc_final: 0.6209 (mtmm) REVERT: D 86 ARG cc_start: 0.6453 (mtp180) cc_final: 0.5717 (ptt180) REVERT: D 93 ASP cc_start: 0.7192 (t0) cc_final: 0.6477 (m-30) REVERT: D 109 PHE cc_start: 0.7282 (m-10) cc_final: 0.7001 (m-80) REVERT: D 125 LYS cc_start: 0.7344 (mmtt) cc_final: 0.6287 (tttt) REVERT: D 162 MET cc_start: 0.8668 (tpt) cc_final: 0.7892 (mmm) REVERT: D 215 ARG cc_start: 0.6587 (ptt180) cc_final: 0.6053 (mtm110) REVERT: D 238 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6360 (tmt) REVERT: D 248 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7533 (mt) REVERT: D 294 HIS cc_start: 0.6541 (m-70) cc_final: 0.6192 (m-70) REVERT: D 307 GLN cc_start: 0.7574 (mt0) cc_final: 0.7343 (mm110) REVERT: D 330 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6169 (mm) REVERT: D 333 LYS cc_start: 0.6132 (OUTLIER) cc_final: 0.5327 (tptp) REVERT: D 395 PRO cc_start: 0.7001 (Cg_endo) cc_final: 0.6702 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5038 (OUTLIER) cc_final: 0.4484 (tp) outliers start: 140 outliers final: 62 residues processed: 316 average time/residue: 1.0153 time to fit residues: 360.4927 Evaluate side-chains 280 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 201 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 294 HIS B 491 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15846 Z= 0.318 Angle : 0.667 9.987 21476 Z= 0.347 Chirality : 0.046 0.257 2422 Planarity : 0.004 0.046 2688 Dihedral : 10.354 111.780 2252 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 7.27 % Allowed : 27.65 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1870 helix: -0.31 (0.15), residues: 1154 sheet: -1.61 (0.52), residues: 100 loop : -0.77 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 246 HIS 0.007 0.001 HIS B 294 PHE 0.016 0.002 PHE D 272 TYR 0.020 0.002 TYR B 364 ARG 0.009 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 201 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7467 (t70) cc_final: 0.7189 (t0) REVERT: A 122 ASP cc_start: 0.7130 (p0) cc_final: 0.6852 (p0) REVERT: A 125 LYS cc_start: 0.6503 (tppt) cc_final: 0.5910 (ttmm) REVERT: A 162 MET cc_start: 0.8110 (tpt) cc_final: 0.7619 (mmm) REVERT: A 183 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6162 (t160) REVERT: A 267 MET cc_start: 0.8447 (mtt) cc_final: 0.7991 (mtm) REVERT: A 298 ARG cc_start: 0.7347 (ttp-170) cc_final: 0.6966 (ttm-80) REVERT: A 339 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5649 (mt-10) REVERT: A 466 ASN cc_start: 0.4534 (OUTLIER) cc_final: 0.4264 (p0) REVERT: A 497 ASP cc_start: 0.6173 (OUTLIER) cc_final: 0.5924 (p0) REVERT: A 510 MET cc_start: -0.0303 (mtt) cc_final: -0.1083 (ptm) REVERT: B 58 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7414 (tpt-90) REVERT: B 83 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6805 (mtm110) REVERT: B 84 LYS cc_start: 0.7811 (pttm) cc_final: 0.7546 (ptmm) REVERT: B 86 ARG cc_start: 0.6553 (mtp180) cc_final: 0.5833 (ptt180) REVERT: B 93 ASP cc_start: 0.7328 (t0) cc_final: 0.6581 (m-30) REVERT: B 109 PHE cc_start: 0.7002 (m-10) cc_final: 0.6754 (m-80) REVERT: B 248 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 307 GLN cc_start: 0.7480 (pp30) cc_final: 0.7208 (tp40) REVERT: B 337 ASP cc_start: 0.6819 (m-30) cc_final: 0.6595 (m-30) REVERT: B 397 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6594 (tp30) REVERT: B 401 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.4300 (mt) REVERT: B 485 MET cc_start: 0.4380 (tpt) cc_final: 0.3525 (mmt) REVERT: B 500 MET cc_start: 0.3775 (ppp) cc_final: 0.3339 (pp-130) REVERT: C 93 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: C 103 ASP cc_start: 0.7483 (t70) cc_final: 0.7127 (t0) REVERT: C 113 LEU cc_start: 0.7689 (mm) cc_final: 0.7452 (tp) REVERT: C 151 ARG cc_start: 0.7322 (ttm110) cc_final: 0.6875 (ppt170) REVERT: C 155 GLN cc_start: 0.7721 (mm110) cc_final: 0.7311 (mp10) REVERT: C 177 ARG cc_start: 0.6995 (mtm110) cc_final: 0.6667 (ttp-110) REVERT: C 179 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6668 (mm-30) REVERT: C 182 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6789 (ttm-80) REVERT: C 183 ASN cc_start: 0.6895 (m-40) cc_final: 0.6373 (t160) REVERT: C 232 LEU cc_start: 0.8381 (mt) cc_final: 0.8078 (mm) REVERT: C 267 MET cc_start: 0.8437 (mtt) cc_final: 0.7981 (mtm) REVERT: C 288 MET cc_start: 0.7984 (tpt) cc_final: 0.7426 (tpp) REVERT: C 298 ARG cc_start: 0.6767 (mtp-110) cc_final: 0.6028 (ttm-80) REVERT: C 356 SER cc_start: 0.7209 (t) cc_final: 0.7002 (p) REVERT: C 388 MET cc_start: 0.4607 (mtt) cc_final: 0.4379 (mtp) REVERT: C 392 TYR cc_start: 0.7586 (m-80) cc_final: 0.7322 (m-80) REVERT: C 494 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.4382 (mp0) REVERT: D 56 LYS cc_start: 0.6669 (tmtt) cc_final: 0.5991 (mtmm) REVERT: D 58 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7330 (tpt-90) REVERT: D 59 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6990 (pt) REVERT: D 86 ARG cc_start: 0.6524 (mtp180) cc_final: 0.5747 (ptt180) REVERT: D 93 ASP cc_start: 0.7198 (t0) cc_final: 0.6538 (m-30) REVERT: D 109 PHE cc_start: 0.7189 (m-10) cc_final: 0.6943 (m-80) REVERT: D 125 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6155 (tttt) REVERT: D 215 ARG cc_start: 0.6519 (ptt180) cc_final: 0.6056 (mtm110) REVERT: D 248 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7396 (mt) REVERT: D 294 HIS cc_start: 0.6537 (m-70) cc_final: 0.6134 (m-70) REVERT: D 317 HIS cc_start: 0.5184 (OUTLIER) cc_final: 0.4252 (p-80) REVERT: D 330 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6409 (mm) REVERT: D 333 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5296 (tptp) REVERT: D 395 PRO cc_start: 0.7103 (Cg_endo) cc_final: 0.6795 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4590 (tp) outliers start: 122 outliers final: 59 residues processed: 296 average time/residue: 1.1093 time to fit residues: 366.5913 Evaluate side-chains 275 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 198 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ASN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 294 HIS B 490 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 360 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15846 Z= 0.214 Angle : 0.625 9.947 21476 Z= 0.321 Chirality : 0.044 0.232 2422 Planarity : 0.004 0.047 2688 Dihedral : 9.851 113.459 2246 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.56 % Allowed : 27.35 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1870 helix: 0.06 (0.15), residues: 1154 sheet: -1.48 (0.51), residues: 100 loop : -0.57 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 73 HIS 0.006 0.001 HIS B 294 PHE 0.021 0.001 PHE A 409 TYR 0.023 0.002 TYR D 364 ARG 0.011 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 203 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6825 (mmt90) cc_final: 0.6623 (mpt-90) REVERT: A 103 ASP cc_start: 0.7559 (t70) cc_final: 0.7258 (t0) REVERT: A 122 ASP cc_start: 0.7059 (p0) cc_final: 0.6668 (p0) REVERT: A 162 MET cc_start: 0.8108 (tpt) cc_final: 0.7678 (mmm) REVERT: A 183 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6176 (t160) REVERT: A 267 MET cc_start: 0.8456 (mtt) cc_final: 0.7996 (mtm) REVERT: A 298 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.6988 (tmm-80) REVERT: A 339 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5754 (mt-10) REVERT: A 441 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4974 (tm-30) REVERT: A 464 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5751 (ttp-110) REVERT: A 510 MET cc_start: 0.0003 (mtt) cc_final: -0.0850 (ptm) REVERT: B 58 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7386 (tpt-90) REVERT: B 59 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7130 (pt) REVERT: B 83 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: B 84 LYS cc_start: 0.7779 (pttm) cc_final: 0.7563 (ptmm) REVERT: B 86 ARG cc_start: 0.6418 (mtp180) cc_final: 0.5699 (ptt180) REVERT: B 93 ASP cc_start: 0.7301 (t0) cc_final: 0.6605 (m-30) REVERT: B 109 PHE cc_start: 0.6972 (m-10) cc_final: 0.6730 (m-80) REVERT: B 133 ARG cc_start: 0.6930 (mtp180) cc_final: 0.6643 (mtm110) REVERT: B 248 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 307 GLN cc_start: 0.7496 (pp30) cc_final: 0.7272 (tp40) REVERT: B 315 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6584 (tmt-80) REVERT: B 337 ASP cc_start: 0.6804 (m-30) cc_final: 0.6562 (m-30) REVERT: B 397 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6634 (tp30) REVERT: B 400 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4710 (tp) REVERT: B 485 MET cc_start: 0.4357 (tpt) cc_final: 0.3647 (mmt) REVERT: B 500 MET cc_start: 0.3552 (ppp) cc_final: 0.3128 (pp-130) REVERT: C 93 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: C 103 ASP cc_start: 0.7446 (t70) cc_final: 0.7113 (t0) REVERT: C 113 LEU cc_start: 0.7741 (mm) cc_final: 0.7491 (tp) REVERT: C 155 GLN cc_start: 0.7708 (mm110) cc_final: 0.7309 (mp10) REVERT: C 177 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6690 (ttp-110) REVERT: C 179 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6654 (mm-30) REVERT: C 182 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7166 (ttm-80) REVERT: C 183 ASN cc_start: 0.6887 (m-40) cc_final: 0.6337 (t160) REVERT: C 185 ASN cc_start: 0.6843 (OUTLIER) cc_final: 0.5800 (t0) REVERT: C 232 LEU cc_start: 0.8360 (mt) cc_final: 0.8078 (mm) REVERT: C 267 MET cc_start: 0.8425 (mtt) cc_final: 0.7943 (mtm) REVERT: C 288 MET cc_start: 0.7964 (tpt) cc_final: 0.7509 (tpp) REVERT: C 298 ARG cc_start: 0.6755 (mtp-110) cc_final: 0.6049 (ttm-80) REVERT: C 392 TYR cc_start: 0.7615 (m-80) cc_final: 0.7371 (m-80) REVERT: C 494 GLU cc_start: 0.4567 (OUTLIER) cc_final: 0.4347 (mp0) REVERT: D 56 LYS cc_start: 0.6761 (tmtt) cc_final: 0.5970 (mtmm) REVERT: D 58 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7299 (tpt-90) REVERT: D 59 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7015 (pt) REVERT: D 86 ARG cc_start: 0.6449 (mtp180) cc_final: 0.5691 (ptt180) REVERT: D 93 ASP cc_start: 0.7180 (t0) cc_final: 0.6648 (m-30) REVERT: D 109 PHE cc_start: 0.7212 (m-10) cc_final: 0.6961 (m-80) REVERT: D 215 ARG cc_start: 0.6440 (ptt180) cc_final: 0.5918 (mtm110) REVERT: D 248 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7651 (mm) REVERT: D 294 HIS cc_start: 0.6550 (m-70) cc_final: 0.6131 (m-70) REVERT: D 317 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.4178 (p-80) REVERT: D 330 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6370 (mm) REVERT: D 333 LYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5280 (tptp) REVERT: D 395 PRO cc_start: 0.7095 (Cg_endo) cc_final: 0.6797 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4884 (OUTLIER) cc_final: 0.4587 (tp) outliers start: 110 outliers final: 52 residues processed: 286 average time/residue: 1.0564 time to fit residues: 337.9130 Evaluate side-chains 269 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 197 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 294 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15846 Z= 0.234 Angle : 0.629 9.508 21476 Z= 0.322 Chirality : 0.044 0.201 2422 Planarity : 0.004 0.043 2688 Dihedral : 9.144 83.312 2236 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.44 % Allowed : 27.35 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1870 helix: 0.22 (0.15), residues: 1154 sheet: -1.36 (0.52), residues: 100 loop : -0.48 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 246 HIS 0.006 0.001 HIS B 294 PHE 0.012 0.001 PHE D 272 TYR 0.022 0.002 TYR D 364 ARG 0.011 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 205 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6823 (mmt90) cc_final: 0.6564 (mmt90) REVERT: A 103 ASP cc_start: 0.7545 (t70) cc_final: 0.7229 (t0) REVERT: A 106 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6201 (tmm) REVERT: A 122 ASP cc_start: 0.7047 (p0) cc_final: 0.6601 (p0) REVERT: A 162 MET cc_start: 0.8100 (tpt) cc_final: 0.7606 (mmm) REVERT: A 183 ASN cc_start: 0.6821 (m-40) cc_final: 0.6168 (t160) REVERT: A 267 MET cc_start: 0.8457 (mtt) cc_final: 0.8007 (mtm) REVERT: A 298 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6941 (tmm-80) REVERT: A 441 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4871 (tm-30) REVERT: A 451 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4751 (mt) REVERT: A 510 MET cc_start: -0.0195 (mtt) cc_final: -0.1055 (ptm) REVERT: B 46 ARG cc_start: 0.5328 (ttm110) cc_final: 0.5044 (ttm-80) REVERT: B 58 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7341 (tpt-90) REVERT: B 59 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7075 (pt) REVERT: B 83 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6713 (mtm110) REVERT: B 86 ARG cc_start: 0.6510 (mtp180) cc_final: 0.5710 (ptt180) REVERT: B 93 ASP cc_start: 0.7230 (t0) cc_final: 0.6550 (m-30) REVERT: B 109 PHE cc_start: 0.6853 (m-10) cc_final: 0.6622 (m-80) REVERT: B 162 MET cc_start: 0.8630 (tpt) cc_final: 0.8083 (mmm) REVERT: B 248 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7873 (mt) REVERT: B 315 ARG cc_start: 0.7074 (mmm160) cc_final: 0.5927 (tpt170) REVERT: B 337 ASP cc_start: 0.6807 (m-30) cc_final: 0.6584 (m-30) REVERT: B 398 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.6089 (p0) REVERT: B 400 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4754 (tp) REVERT: B 485 MET cc_start: 0.4338 (tpt) cc_final: 0.3599 (mmp) REVERT: B 500 MET cc_start: 0.3541 (ppp) cc_final: 0.3104 (pp-130) REVERT: C 93 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: C 103 ASP cc_start: 0.7401 (t70) cc_final: 0.7088 (t0) REVERT: C 155 GLN cc_start: 0.7633 (mm110) cc_final: 0.7271 (mp10) REVERT: C 177 ARG cc_start: 0.6880 (mtm110) cc_final: 0.6585 (ttp-110) REVERT: C 179 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 182 ARG cc_start: 0.7413 (ttm110) cc_final: 0.7028 (ttm-80) REVERT: C 183 ASN cc_start: 0.6922 (m-40) cc_final: 0.6362 (t160) REVERT: C 185 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.5741 (t0) REVERT: C 232 LEU cc_start: 0.8380 (mt) cc_final: 0.8071 (mm) REVERT: C 267 MET cc_start: 0.8425 (mtt) cc_final: 0.7946 (mtm) REVERT: C 288 MET cc_start: 0.7976 (tpt) cc_final: 0.7512 (tpp) REVERT: C 298 ARG cc_start: 0.6726 (mtp-110) cc_final: 0.6031 (ttm-80) REVERT: C 392 TYR cc_start: 0.7668 (m-80) cc_final: 0.7400 (m-80) REVERT: C 494 GLU cc_start: 0.4574 (OUTLIER) cc_final: 0.4339 (mp0) REVERT: D 56 LYS cc_start: 0.6748 (tmtt) cc_final: 0.5907 (mtmm) REVERT: D 58 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7214 (tpt-90) REVERT: D 59 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6964 (pt) REVERT: D 86 ARG cc_start: 0.6436 (mtp180) cc_final: 0.5673 (ptt180) REVERT: D 93 ASP cc_start: 0.7197 (t0) cc_final: 0.6646 (m-30) REVERT: D 105 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7736 (pp) REVERT: D 109 PHE cc_start: 0.7203 (m-10) cc_final: 0.6955 (m-80) REVERT: D 215 ARG cc_start: 0.6438 (ptt180) cc_final: 0.5911 (mtm110) REVERT: D 248 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7648 (mm) REVERT: D 294 HIS cc_start: 0.6563 (m-70) cc_final: 0.6147 (m-70) REVERT: D 317 HIS cc_start: 0.5183 (OUTLIER) cc_final: 0.4343 (p-80) REVERT: D 330 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6334 (mm) REVERT: D 333 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5269 (tptp) REVERT: D 395 PRO cc_start: 0.7043 (Cg_endo) cc_final: 0.6755 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: D 400 ILE cc_start: 0.4904 (OUTLIER) cc_final: 0.4614 (tp) REVERT: D 495 MET cc_start: 0.4979 (pp-130) cc_final: 0.4658 (pp-130) REVERT: D 500 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.5001 (tmm) outliers start: 108 outliers final: 52 residues processed: 290 average time/residue: 1.0870 time to fit residues: 351.4612 Evaluate side-chains 274 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 200 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 403 ASN B 218 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS C 360 HIS D 472 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15846 Z= 0.193 Angle : 0.605 10.133 21476 Z= 0.310 Chirality : 0.043 0.196 2422 Planarity : 0.004 0.046 2688 Dihedral : 8.747 80.134 2229 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.84 % Allowed : 27.95 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1870 helix: 0.44 (0.15), residues: 1152 sheet: -1.34 (0.51), residues: 100 loop : -0.37 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 73 HIS 0.005 0.001 HIS D 329 PHE 0.021 0.001 PHE A 409 TYR 0.026 0.002 TYR B 364 ARG 0.013 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 209 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7584 (t70) cc_final: 0.7279 (t0) REVERT: A 106 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6266 (tmm) REVERT: A 122 ASP cc_start: 0.6910 (p0) cc_final: 0.6469 (p0) REVERT: A 162 MET cc_start: 0.8099 (tpt) cc_final: 0.7626 (mmm) REVERT: A 183 ASN cc_start: 0.6778 (m-40) cc_final: 0.6142 (t160) REVERT: A 267 MET cc_start: 0.8463 (mtt) cc_final: 0.8012 (mtm) REVERT: A 298 ARG cc_start: 0.7282 (ttp-170) cc_final: 0.6946 (ttm-80) REVERT: A 441 GLU cc_start: 0.5062 (OUTLIER) cc_final: 0.4658 (tt0) REVERT: A 510 MET cc_start: -0.0372 (mtt) cc_final: -0.1180 (ptm) REVERT: B 46 ARG cc_start: 0.5413 (ttm110) cc_final: 0.5059 (ttm-80) REVERT: B 58 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7305 (tpt-90) REVERT: B 59 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7166 (pt) REVERT: B 83 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6710 (mtm110) REVERT: B 86 ARG cc_start: 0.6396 (mtp180) cc_final: 0.5617 (ptt180) REVERT: B 93 ASP cc_start: 0.7186 (t0) cc_final: 0.6537 (m-30) REVERT: B 109 PHE cc_start: 0.6798 (m-10) cc_final: 0.6574 (m-80) REVERT: B 115 LYS cc_start: 0.7740 (tppt) cc_final: 0.7390 (tppt) REVERT: B 133 ARG cc_start: 0.6822 (mtp180) cc_final: 0.6573 (mtm110) REVERT: B 162 MET cc_start: 0.8653 (tpt) cc_final: 0.8282 (mmm) REVERT: B 248 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7851 (mt) REVERT: B 337 ASP cc_start: 0.6713 (m-30) cc_final: 0.6459 (m-30) REVERT: B 400 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4762 (tp) REVERT: B 485 MET cc_start: 0.4493 (tpt) cc_final: 0.3729 (mmt) REVERT: B 500 MET cc_start: 0.3629 (ppp) cc_final: 0.3146 (tpt) REVERT: C 53 TYR cc_start: 0.8033 (m-80) cc_final: 0.6752 (m-80) REVERT: C 58 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.5504 (mpt-90) REVERT: C 93 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: C 103 ASP cc_start: 0.7360 (t70) cc_final: 0.7073 (t0) REVERT: C 155 GLN cc_start: 0.7623 (mm110) cc_final: 0.7271 (mp10) REVERT: C 177 ARG cc_start: 0.6846 (mtm110) cc_final: 0.6555 (ttp-110) REVERT: C 179 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 182 ARG cc_start: 0.7289 (ttm110) cc_final: 0.7049 (ttm-80) REVERT: C 183 ASN cc_start: 0.6810 (m-40) cc_final: 0.6343 (t160) REVERT: C 185 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.5867 (t0) REVERT: C 232 LEU cc_start: 0.8462 (mt) cc_final: 0.8122 (mm) REVERT: C 267 MET cc_start: 0.8435 (mtt) cc_final: 0.7972 (mtm) REVERT: C 288 MET cc_start: 0.8008 (tpt) cc_final: 0.7576 (tpp) REVERT: C 298 ARG cc_start: 0.6728 (mtp-110) cc_final: 0.6053 (ttm-80) REVERT: C 392 TYR cc_start: 0.7707 (m-80) cc_final: 0.7434 (m-80) REVERT: C 432 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6475 (pp20) REVERT: C 494 GLU cc_start: 0.4562 (OUTLIER) cc_final: 0.4328 (mp0) REVERT: D 58 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7185 (tpt-90) REVERT: D 59 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7067 (pt) REVERT: D 86 ARG cc_start: 0.6414 (mtp180) cc_final: 0.5662 (ptt180) REVERT: D 93 ASP cc_start: 0.7186 (t0) cc_final: 0.6668 (m-30) REVERT: D 105 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7702 (pt) REVERT: D 109 PHE cc_start: 0.7168 (m-10) cc_final: 0.6929 (m-80) REVERT: D 215 ARG cc_start: 0.6352 (ptt180) cc_final: 0.5859 (mtm110) REVERT: D 248 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7620 (mm) REVERT: D 294 HIS cc_start: 0.6554 (m-70) cc_final: 0.6134 (m-70) REVERT: D 317 HIS cc_start: 0.5140 (OUTLIER) cc_final: 0.4329 (p-80) REVERT: D 330 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6307 (mm) REVERT: D 333 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5420 (tptp) REVERT: D 395 PRO cc_start: 0.7097 (Cg_endo) cc_final: 0.6818 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: D 400 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4620 (tp) outliers start: 98 outliers final: 46 residues processed: 281 average time/residue: 1.1912 time to fit residues: 371.4768 Evaluate side-chains 268 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 201 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS D 472 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15846 Z= 0.243 Angle : 0.624 10.661 21476 Z= 0.318 Chirality : 0.044 0.202 2422 Planarity : 0.004 0.047 2688 Dihedral : 8.720 79.955 2229 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.02 % Allowed : 28.13 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1870 helix: 0.45 (0.15), residues: 1152 sheet: -1.29 (0.51), residues: 100 loop : -0.35 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.019 0.001 PHE C 409 TYR 0.026 0.002 TYR B 364 ARG 0.013 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 197 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7597 (t70) cc_final: 0.7297 (t0) REVERT: A 106 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: A 122 ASP cc_start: 0.6915 (p0) cc_final: 0.6469 (p0) REVERT: A 125 LYS cc_start: 0.6392 (tppt) cc_final: 0.5860 (ttmm) REVERT: A 162 MET cc_start: 0.8088 (tpt) cc_final: 0.7615 (mmm) REVERT: A 183 ASN cc_start: 0.6781 (m-40) cc_final: 0.6135 (t160) REVERT: A 267 MET cc_start: 0.8458 (mtt) cc_final: 0.8009 (mtm) REVERT: A 298 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.6916 (ttm-80) REVERT: A 441 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.4605 (tt0) REVERT: A 510 MET cc_start: -0.0431 (mtt) cc_final: -0.1260 (ptm) REVERT: B 46 ARG cc_start: 0.5434 (ttm110) cc_final: 0.5079 (ttm-80) REVERT: B 58 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7328 (tpt-90) REVERT: B 59 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7160 (pt) REVERT: B 83 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6723 (mtm110) REVERT: B 86 ARG cc_start: 0.6402 (mtp180) cc_final: 0.5619 (ptt180) REVERT: B 93 ASP cc_start: 0.7202 (t0) cc_final: 0.6553 (m-30) REVERT: B 109 PHE cc_start: 0.6780 (m-10) cc_final: 0.6559 (m-80) REVERT: B 115 LYS cc_start: 0.7717 (tppt) cc_final: 0.7349 (tppt) REVERT: B 162 MET cc_start: 0.8662 (tpt) cc_final: 0.8184 (mmm) REVERT: B 248 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7871 (mt) REVERT: B 315 ARG cc_start: 0.7153 (mmm160) cc_final: 0.5974 (tpt170) REVERT: B 337 ASP cc_start: 0.6818 (m-30) cc_final: 0.6590 (m-30) REVERT: B 397 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: B 485 MET cc_start: 0.4499 (tpt) cc_final: 0.3733 (mmt) REVERT: B 500 MET cc_start: 0.3492 (ppp) cc_final: 0.3081 (pp-130) REVERT: C 58 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.5504 (mpt-90) REVERT: C 93 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: C 103 ASP cc_start: 0.7412 (t70) cc_final: 0.7135 (t0) REVERT: C 155 GLN cc_start: 0.7561 (mm110) cc_final: 0.7212 (mp10) REVERT: C 177 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6509 (ttp-110) REVERT: C 179 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 182 ARG cc_start: 0.7347 (ttm110) cc_final: 0.7107 (ttm-80) REVERT: C 183 ASN cc_start: 0.6823 (m-40) cc_final: 0.6336 (t160) REVERT: C 185 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.5885 (t0) REVERT: C 267 MET cc_start: 0.8440 (mtt) cc_final: 0.7953 (mtm) REVERT: C 288 MET cc_start: 0.7980 (tpt) cc_final: 0.7520 (tpp) REVERT: C 298 ARG cc_start: 0.6726 (mtp-110) cc_final: 0.6096 (ttm-80) REVERT: C 392 TYR cc_start: 0.7702 (m-80) cc_final: 0.7395 (m-80) REVERT: C 432 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6452 (pp20) REVERT: C 494 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.4327 (mp0) REVERT: D 58 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7205 (tpt-90) REVERT: D 59 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7008 (pt) REVERT: D 86 ARG cc_start: 0.6437 (mtp180) cc_final: 0.5658 (ptt180) REVERT: D 93 ASP cc_start: 0.7194 (t0) cc_final: 0.6679 (m-30) REVERT: D 105 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7703 (pt) REVERT: D 109 PHE cc_start: 0.7170 (m-10) cc_final: 0.6925 (m-80) REVERT: D 215 ARG cc_start: 0.6397 (ptt180) cc_final: 0.5907 (mmm160) REVERT: D 248 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7652 (mm) REVERT: D 294 HIS cc_start: 0.6558 (m-70) cc_final: 0.6128 (m-70) REVERT: D 317 HIS cc_start: 0.5141 (OUTLIER) cc_final: 0.4321 (p-80) REVERT: D 330 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6218 (mm) REVERT: D 333 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5415 (tptp) REVERT: D 387 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7169 (pt0) REVERT: D 395 PRO cc_start: 0.7032 (Cg_endo) cc_final: 0.6745 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: D 400 ILE cc_start: 0.4946 (OUTLIER) cc_final: 0.4648 (tp) REVERT: D 500 MET cc_start: 0.5284 (OUTLIER) cc_final: 0.5036 (tmm) outliers start: 101 outliers final: 53 residues processed: 273 average time/residue: 1.1496 time to fit residues: 348.6584 Evaluate side-chains 270 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 195 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.4462 > 50: distance: 60 - 86: 36.648 distance: 66 - 73: 34.827 distance: 67 - 97: 36.426 distance: 75 - 76: 39.766 distance: 75 - 78: 56.775 distance: 79 - 80: 41.326 distance: 79 - 82: 38.513 distance: 81 - 109: 3.165 distance: 82 - 83: 68.138 distance: 82 - 84: 70.320 distance: 86 - 87: 40.993 distance: 87 - 90: 40.534 distance: 88 - 89: 40.432 distance: 89 - 117: 55.929 distance: 90 - 91: 41.104 distance: 92 - 93: 40.573 distance: 93 - 94: 37.408 distance: 94 - 95: 6.395 distance: 94 - 96: 39.535 distance: 97 - 98: 58.031 distance: 98 - 99: 38.838 distance: 98 - 101: 56.637 distance: 99 - 100: 40.084 distance: 99 - 103: 41.105 distance: 101 - 102: 39.437 distance: 103 - 104: 38.938 distance: 104 - 105: 41.226 distance: 104 - 107: 46.541 distance: 105 - 109: 41.106 distance: 106 - 133: 54.350 distance: 107 - 108: 14.215 distance: 109 - 110: 56.648 distance: 110 - 111: 11.006 distance: 110 - 113: 40.116 distance: 111 - 112: 3.388 distance: 111 - 117: 12.923 distance: 112 - 144: 56.501 distance: 113 - 114: 58.595 distance: 113 - 115: 56.173 distance: 114 - 116: 12.395 distance: 118 - 119: 38.930 distance: 119 - 120: 39.715 distance: 119 - 123: 40.326 distance: 123 - 124: 41.009 distance: 124 - 125: 32.276 distance: 125 - 126: 9.347 distance: 125 - 133: 31.201 distance: 128 - 129: 56.087 distance: 128 - 130: 39.708 distance: 129 - 131: 16.493 distance: 130 - 132: 7.850 distance: 131 - 132: 37.871 distance: 134 - 135: 39.256 distance: 135 - 136: 8.423 distance: 138 - 140: 9.384 distance: 139 - 141: 20.429 distance: 140 - 142: 32.413 distance: 141 - 143: 40.082 distance: 142 - 143: 6.088 distance: 144 - 145: 41.261 distance: 146 - 152: 34.187 distance: 148 - 149: 56.608 distance: 149 - 150: 39.888