Starting phenix.real_space_refine on Fri Feb 16 13:37:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/02_2024/7wm2_32598_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/02_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_32598/02_2024/7wm2_32598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/02_2024/7wm2_32598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/02_2024/7wm2_32598_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/02_2024/7wm2_32598_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.23, per 1000 atoms: 0.53 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: 6.36 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 82 helices and 8 sheets defined 60.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 55 through 81 Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 92 through 108 removed outlier: 3.803A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.505A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 4.013A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 4.300A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 161 No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.436A pdb=" N ARG A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 215 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 264 through 315 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) Processing helix chain 'A' and resid 320 through 337 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 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 352 through 369 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) removed outlier: 5.195A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.823A pdb=" N ILE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 498 through 512 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) removed outlier: 3.892A pdb=" N MET A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 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 87 through 94 removed outlier: 4.972A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 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) removed outlier: 4.180A pdb=" N PHE B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 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 136 through 141 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.650A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 179 removed outlier: 4.157A pdb=" N TYR B 157 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY B 158 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE B 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 172 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 176 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 214 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 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 264 through 293 Processing helix chain 'B' and resid 297 through 316 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 320 through 345 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 352 through 362 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 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.581A pdb=" N GLN B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 446 No H-bonds generated for 'chain 'B' and resid 443 through 446' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.628A pdb=" N ILE B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 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 501 through 510 removed outlier: 3.877A pdb=" N GLU B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 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 87 through 105 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 124 through 132 removed outlier: 3.571A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 removed outlier: 3.981A pdb=" N THR C 143 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 4.190A pdb=" N ARG C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 179 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) removed outlier: 3.598A pdb=" N ALA C 173 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 215 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 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 236 through 251 removed outlier: 3.602A pdb=" N ILE C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 295 removed outlier: 3.574A pdb=" N PHE C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 315 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) Processing helix chain 'C' and resid 320 through 339 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 345 through 349 Processing helix chain 'C' and resid 352 through 369 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) removed outlier: 4.966A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 467 through 476 removed outlier: 4.011A pdb=" N ILE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 494 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 502 through 508 Processing helix chain 'D' and resid 55 through 81 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 87 through 94 removed outlier: 4.816A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 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 124 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 136 through 143 removed outlier: 4.252A pdb=" N THR D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 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 154 through 178 removed outlier: 4.143A pdb=" N TYR D 157 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLY D 158 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 160 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG D 164 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 172 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 176 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 214 removed outlier: 3.807A pdb=" N ALA D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 293 Processing helix chain 'D' and resid 300 through 316 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) removed outlier: 3.588A pdb=" N ASN D 316 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 348 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 352 through 361 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 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 378 through 386 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) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.874A pdb=" N LEU D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 474 removed outlier: 3.556A pdb=" N ILE D 474 " --> pdb=" O PHE D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 494 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 498 through 511 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= A, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.552A pdb=" N LEU A 463 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 412 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET A 465 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR A 410 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 453 through 456 Processing sheet with id= C, first strand: chain 'B' and resid 391 through 393 Processing sheet with id= D, first strand: chain 'B' and resid 417 through 420 Processing sheet with id= E, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.672A pdb=" N LEU C 463 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU C 412 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET C 465 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR C 410 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 453 through 456 removed outlier: 3.585A pdb=" N VAL C 420 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 423 " --> pdb=" O THR C 426 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 391 through 393 removed outlier: 3.506A pdb=" N GLN D 461 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN D 414 " --> pdb=" O GLN D 461 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 463 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU D 412 " --> pdb=" O LEU D 463 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 432 through 434 703 hydrogen bonds defined for protein. 1899 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: 4.44 Time building geometry restraints manager: 6.89 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: 1437 2.72 - 3.32: 19333 3.32 - 3.93: 28988 3.93 - 4.53: 40961 4.53 - 5.14: 60156 Nonbonded interactions: 150875 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 150870 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.890 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 44.180 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.310 ------------------------------------------------------------------------------- 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= 0.756 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 : 1.909 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: 1.1803 time to fit residues: 558.8005 Evaluate side-chains 307 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 217 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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: 0.6980 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 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: 0.8784 ------------------------------------------------------------------------------- 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 216 ASN B 218 ASN B 290 ASN B 294 HIS B 343 GLN B 472 ASN B 475 GLN 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15846 Z= 0.200 Angle : 0.690 10.685 21476 Z= 0.354 Chirality : 0.044 0.176 2422 Planarity : 0.005 0.037 2688 Dihedral : 12.217 100.186 2384 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 7.99 % Allowed : 26.10 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.18), residues: 1870 helix: -1.17 (0.14), residues: 1138 sheet: -2.36 (0.53), residues: 90 loop : -1.20 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 135 HIS 0.007 0.001 HIS D 491 PHE 0.015 0.001 PHE C 187 TYR 0.019 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 362 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 228 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7400 (t70) cc_final: 0.7123 (t0) REVERT: A 162 MET cc_start: 0.8419 (tpt) cc_final: 0.7970 (tpt) REVERT: A 183 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6017 (t160) REVERT: A 194 LEU cc_start: 0.7677 (mt) cc_final: 0.7399 (mt) REVERT: A 232 LEU cc_start: 0.8542 (mt) cc_final: 0.8271 (mm) REVERT: A 267 MET cc_start: 0.8410 (mtt) cc_final: 0.7994 (mtm) REVERT: A 298 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7012 (ttm-80) REVERT: A 339 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5586 (mt-10) REVERT: A 356 SER cc_start: 0.7348 (t) cc_final: 0.7129 (p) REVERT: A 510 MET cc_start: 0.0440 (mtt) cc_final: -0.0621 (ttt) REVERT: B 83 ARG cc_start: 0.7226 (ptp-110) cc_final: 0.6860 (mtm110) REVERT: B 86 ARG cc_start: 0.6677 (mtp180) cc_final: 0.6025 (ptt180) REVERT: B 93 ASP cc_start: 0.7281 (t0) cc_final: 0.6469 (m-30) REVERT: B 105 ILE cc_start: 0.7808 (mt) cc_final: 0.7570 (mt) REVERT: B 109 PHE cc_start: 0.7031 (m-10) cc_final: 0.6748 (m-80) REVERT: B 301 ASN cc_start: 0.5192 (OUTLIER) cc_final: 0.4898 (OUTLIER) REVERT: B 337 ASP cc_start: 0.6719 (m-30) cc_final: 0.6468 (m-30) REVERT: B 352 LYS cc_start: 0.5717 (OUTLIER) cc_final: 0.4617 (tmtt) REVERT: B 387 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7029 (pt0) REVERT: B 397 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6364 (tp30) REVERT: B 485 MET cc_start: 0.4470 (tpt) cc_final: 0.3548 (mmp) REVERT: C 58 ARG cc_start: 0.7522 (mmt90) cc_final: 0.7037 (mmt90) REVERT: C 93 ASP cc_start: 0.7844 (t0) cc_final: 0.7506 (m-30) REVERT: C 103 ASP cc_start: 0.7439 (t70) cc_final: 0.7060 (t0) REVERT: C 113 LEU cc_start: 0.7645 (mm) cc_final: 0.7331 (tp) REVERT: C 122 ASP cc_start: 0.6569 (p0) cc_final: 0.6297 (p0) REVERT: C 151 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6903 (ppt170) REVERT: C 155 GLN cc_start: 0.7688 (mm110) cc_final: 0.7277 (mp10) REVERT: C 183 ASN cc_start: 0.6853 (m-40) cc_final: 0.6593 (t160) REVERT: C 194 LEU cc_start: 0.7375 (mt) cc_final: 0.7164 (mt) REVERT: C 248 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 267 MET cc_start: 0.8345 (mtt) cc_final: 0.8048 (mtt) REVERT: C 288 MET cc_start: 0.7844 (tpt) cc_final: 0.7449 (tpp) REVERT: C 343 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.4270 (pp30) REVERT: C 388 MET cc_start: 0.5176 (mtt) cc_final: 0.4900 (mtm) REVERT: C 401 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6344 (pp) REVERT: C 441 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5345 (tt0) REVERT: C 464 ARG cc_start: 0.5475 (ttm170) cc_final: 0.5156 (ttp-110) REVERT: C 497 ASP cc_start: 0.5616 (OUTLIER) cc_final: 0.5240 (p0) REVERT: D 56 LYS cc_start: 0.6612 (tmtt) cc_final: 0.6097 (mtmm) REVERT: D 86 ARG cc_start: 0.6335 (mtp180) cc_final: 0.5665 (ptt180) REVERT: D 93 ASP cc_start: 0.7259 (t0) cc_final: 0.6495 (m-30) REVERT: D 105 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7788 (pt) REVERT: D 109 PHE cc_start: 0.7373 (m-10) cc_final: 0.7140 (m-80) REVERT: D 125 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6373 (tttt) REVERT: D 162 MET cc_start: 0.8395 (tpt) cc_final: 0.8116 (mmm) REVERT: D 215 ARG cc_start: 0.6561 (ptt180) cc_final: 0.6312 (mtm110) REVERT: D 252 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.6881 (t) REVERT: D 294 HIS cc_start: 0.6864 (m-70) cc_final: 0.6505 (m-70) REVERT: D 330 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6336 (mm) REVERT: D 333 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5324 (tptp) REVERT: D 348 ASP cc_start: 0.6322 (p0) cc_final: 0.5981 (p0) REVERT: D 384 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.3490 (mm) REVERT: D 395 PRO cc_start: 0.7145 (Cg_endo) cc_final: 0.6820 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5052 (pm20) outliers start: 134 outliers final: 38 residues processed: 335 average time/residue: 1.0163 time to fit residues: 383.5266 Evaluate side-chains 256 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 202 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 171 VAL 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 452 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 462 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 159 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 VAL 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 336 THR Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL 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 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: 4.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 472 ASN B 218 ASN B 294 HIS B 301 ASN ** 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** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 15846 Z= 0.486 Angle : 0.766 10.809 21476 Z= 0.393 Chirality : 0.051 0.336 2422 Planarity : 0.005 0.048 2688 Dihedral : 10.697 86.616 2263 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 8.10 % Allowed : 26.28 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1870 helix: -0.95 (0.14), residues: 1134 sheet: -2.05 (0.54), residues: 90 loop : -1.01 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 246 HIS 0.006 0.002 HIS A 260 PHE 0.024 0.002 PHE D 272 TYR 0.023 0.003 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 344 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 208 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7347 (t70) cc_final: 0.7027 (t0) REVERT: A 124 ARG cc_start: 0.6797 (mtm110) cc_final: 0.6065 (mtt180) REVERT: A 183 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6122 (t160) REVERT: A 298 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7021 (ttt90) REVERT: A 339 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5655 (mt-10) REVERT: A 356 SER cc_start: 0.7314 (t) cc_final: 0.7091 (p) REVERT: A 408 ASP cc_start: 0.6757 (m-30) cc_final: 0.6436 (m-30) REVERT: A 510 MET cc_start: -0.0022 (mtt) cc_final: -0.1033 (ttt) REVERT: B 46 ARG cc_start: 0.5709 (ttm110) cc_final: 0.5323 (ttm-80) REVERT: B 83 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6915 (mtm110) REVERT: B 84 LYS cc_start: 0.7917 (pttm) cc_final: 0.7598 (ptmm) REVERT: B 86 ARG cc_start: 0.6723 (mtp180) cc_final: 0.5959 (ptt180) REVERT: B 93 ASP cc_start: 0.7332 (t0) cc_final: 0.6539 (m-30) REVERT: B 105 ILE cc_start: 0.7902 (mt) cc_final: 0.7647 (mt) REVERT: B 109 PHE cc_start: 0.7008 (m-10) cc_final: 0.6749 (m-80) REVERT: B 248 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 258 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7264 (p0) REVERT: B 330 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6220 (mm) REVERT: B 337 ASP cc_start: 0.6805 (m-30) cc_final: 0.6551 (m-30) REVERT: B 485 MET cc_start: 0.4417 (tpt) cc_final: 0.3516 (mmt) REVERT: B 500 MET cc_start: 0.3648 (ppp) cc_final: 0.3059 (pp-130) REVERT: C 58 ARG cc_start: 0.7387 (mmt90) cc_final: 0.7172 (mpt-90) REVERT: C 93 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: C 103 ASP cc_start: 0.7459 (t70) cc_final: 0.7042 (t0) REVERT: C 113 LEU cc_start: 0.7655 (mm) cc_final: 0.7373 (tp) REVERT: C 151 ARG cc_start: 0.7310 (ttm110) cc_final: 0.6869 (ppt170) REVERT: C 155 GLN cc_start: 0.7671 (mm110) cc_final: 0.7284 (mp10) REVERT: C 183 ASN cc_start: 0.6732 (m-40) cc_final: 0.6317 (t160) REVERT: C 288 MET cc_start: 0.7986 (tpt) cc_final: 0.7478 (tpp) REVERT: C 298 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.5896 (ttm-80) REVERT: C 392 TYR cc_start: 0.7465 (m-80) cc_final: 0.7229 (m-80) REVERT: C 466 ASN cc_start: 0.5355 (OUTLIER) cc_final: 0.5109 (p0) REVERT: D 56 LYS cc_start: 0.6786 (tmtt) cc_final: 0.6210 (mtmm) REVERT: D 86 ARG cc_start: 0.6506 (mtp180) cc_final: 0.5806 (ptt180) REVERT: D 93 ASP cc_start: 0.7255 (t0) cc_final: 0.6497 (m-30) REVERT: D 109 PHE cc_start: 0.7322 (m-10) cc_final: 0.7044 (m-80) REVERT: D 125 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6402 (pttt) REVERT: D 162 MET cc_start: 0.8483 (tpt) cc_final: 0.8113 (mmm) REVERT: D 215 ARG cc_start: 0.6484 (ptt180) cc_final: 0.6096 (mtm110) REVERT: D 248 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7349 (mt) REVERT: D 294 HIS cc_start: 0.6803 (m-70) cc_final: 0.6465 (m-70) REVERT: D 307 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7086 (mm110) REVERT: D 330 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6231 (mm) REVERT: D 333 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5292 (tptp) REVERT: D 395 PRO cc_start: 0.7066 (Cg_endo) cc_final: 0.6738 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5017 (OUTLIER) cc_final: 0.4704 (tp) REVERT: D 432 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5057 (pm20) outliers start: 136 outliers final: 56 residues processed: 317 average time/residue: 1.0668 time to fit residues: 380.9434 Evaluate side-chains 275 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 205 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 217 SER 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 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 SER 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 258 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 330 LEU 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 497 ASP Chi-restraints excluded: chain B residue 499 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 142 SER Chi-restraints excluded: chain C residue 143 THR 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 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 474 ILE 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 249 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 307 GLN 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 356 SER Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15846 Z= 0.387 Angle : 0.699 10.789 21476 Z= 0.361 Chirality : 0.048 0.259 2422 Planarity : 0.005 0.049 2688 Dihedral : 10.131 86.570 2250 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 7.15 % Allowed : 27.47 % 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: -1.31 (0.19), residues: 1870 helix: -0.68 (0.15), residues: 1128 sheet: -1.96 (0.55), residues: 90 loop : -0.72 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.019 0.002 PHE D 272 TYR 0.021 0.002 TYR D 245 ARG 0.010 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 320 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 200 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7578 (t70) cc_final: 0.7239 (t0) REVERT: A 124 ARG cc_start: 0.6774 (mtm110) cc_final: 0.6047 (mtt180) REVERT: A 183 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6167 (t160) REVERT: A 267 MET cc_start: 0.8470 (mtt) cc_final: 0.7998 (mtm) REVERT: A 298 ARG cc_start: 0.7358 (ttp-170) cc_final: 0.6948 (ttt90) REVERT: A 339 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5657 (mt-10) REVERT: A 356 SER cc_start: 0.7283 (t) cc_final: 0.7052 (p) REVERT: A 408 ASP cc_start: 0.6869 (m-30) cc_final: 0.6528 (m-30) REVERT: A 510 MET cc_start: 0.0559 (OUTLIER) cc_final: -0.0582 (ttt) REVERT: B 46 ARG cc_start: 0.5664 (ttm110) cc_final: 0.5280 (ttm-80) REVERT: B 58 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7428 (tpt-90) REVERT: B 83 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6887 (mtm110) REVERT: B 84 LYS cc_start: 0.7781 (pttm) cc_final: 0.7520 (ptmm) REVERT: B 86 ARG cc_start: 0.6693 (mtp180) cc_final: 0.5908 (ptt180) REVERT: B 93 ASP cc_start: 0.7289 (t0) cc_final: 0.6508 (m-30) REVERT: B 109 PHE cc_start: 0.6971 (m-10) cc_final: 0.6715 (m-80) REVERT: B 164 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7354 (mmt90) REVERT: B 248 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7763 (mt) REVERT: B 337 ASP cc_start: 0.6787 (m-30) cc_final: 0.6508 (m-30) REVERT: B 397 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: B 398 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6444 (p0) REVERT: B 485 MET cc_start: 0.4328 (tpt) cc_final: 0.3527 (mmt) REVERT: B 500 MET cc_start: 0.3355 (ppp) cc_final: 0.2811 (pp-130) REVERT: C 58 ARG cc_start: 0.7455 (mmt90) cc_final: 0.7135 (mpt-90) REVERT: C 93 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: C 103 ASP cc_start: 0.7440 (t70) cc_final: 0.7018 (t0) REVERT: C 113 LEU cc_start: 0.7700 (mm) cc_final: 0.7457 (tp) REVERT: C 151 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6892 (ppt170) REVERT: C 155 GLN cc_start: 0.7650 (mm110) cc_final: 0.7281 (mp10) REVERT: C 183 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (t160) REVERT: C 249 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8017 (m) REVERT: C 267 MET cc_start: 0.8448 (mtt) cc_final: 0.8024 (mtm) REVERT: C 288 MET cc_start: 0.7976 (tpt) cc_final: 0.7426 (tpp) REVERT: C 392 TYR cc_start: 0.7457 (m-80) cc_final: 0.7198 (m-80) REVERT: C 432 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: C 441 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5513 (tt0) REVERT: C 466 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.5262 (p0) REVERT: D 56 LYS cc_start: 0.6669 (tmtt) cc_final: 0.6142 (mtmm) REVERT: D 58 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7411 (ttm170) REVERT: D 86 ARG cc_start: 0.6544 (mtp180) cc_final: 0.5781 (ptt180) REVERT: D 93 ASP cc_start: 0.7219 (t0) cc_final: 0.6494 (m-30) REVERT: D 109 PHE cc_start: 0.7244 (m-10) cc_final: 0.7003 (m-80) REVERT: D 115 LYS cc_start: 0.7910 (tppt) cc_final: 0.7704 (tppt) REVERT: D 125 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6285 (tttt) REVERT: D 162 MET cc_start: 0.8506 (tpt) cc_final: 0.8080 (mmm) REVERT: D 215 ARG cc_start: 0.6511 (ptt180) cc_final: 0.6104 (mtm110) REVERT: D 248 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7407 (mt) REVERT: D 294 HIS cc_start: 0.6733 (m-70) cc_final: 0.6373 (m-70) REVERT: D 307 GLN cc_start: 0.7162 (mt0) cc_final: 0.6948 (mm110) REVERT: D 315 ARG cc_start: 0.6810 (mmm-85) cc_final: 0.5525 (tpm170) REVERT: D 317 HIS cc_start: 0.5258 (OUTLIER) cc_final: 0.4454 (p-80) REVERT: D 330 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6381 (mm) REVERT: D 333 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5301 (tptp) REVERT: D 395 PRO cc_start: 0.7015 (Cg_endo) cc_final: 0.6692 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4852 (OUTLIER) cc_final: 0.4554 (tp) REVERT: D 495 MET cc_start: 0.3657 (pp-130) cc_final: 0.3317 (pp-130) REVERT: D 500 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.5019 (tmm) outliers start: 120 outliers final: 62 residues processed: 294 average time/residue: 1.0522 time to fit residues: 346.4268 Evaluate side-chains 279 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 197 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 110 VAL 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 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 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 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 432 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 474 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 398 ASP 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 92 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 141 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 217 SER 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 249 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 466 ASN 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 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 249 THR 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 366 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 294 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 126 GLN ** 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: 0.6932 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15846 Z= 0.304 Angle : 0.646 9.804 21476 Z= 0.333 Chirality : 0.046 0.246 2422 Planarity : 0.004 0.047 2688 Dihedral : 9.603 79.491 2243 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 7.21 % Allowed : 27.77 % Favored : 65.02 % 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: -0.91 (0.19), residues: 1870 helix: -0.37 (0.15), residues: 1128 sheet: -1.79 (0.56), residues: 90 loop : -0.54 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.018 0.002 PHE A 409 TYR 0.025 0.002 TYR B 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 321 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 200 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7496 (t70) cc_final: 0.7162 (t0) REVERT: A 183 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6170 (t160) REVERT: A 267 MET cc_start: 0.8462 (mtt) cc_final: 0.8036 (mtm) REVERT: A 298 ARG cc_start: 0.7362 (ttp-170) cc_final: 0.6952 (ttt90) REVERT: A 339 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5738 (mt-10) REVERT: A 432 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 508 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6334 (pp20) REVERT: A 510 MET cc_start: 0.0445 (OUTLIER) cc_final: -0.0673 (ttt) REVERT: B 46 ARG cc_start: 0.5592 (ttm110) cc_final: 0.5212 (ttm-80) REVERT: B 58 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7364 (tpt-90) REVERT: B 83 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6775 (mtm110) REVERT: B 84 LYS cc_start: 0.7683 (pttm) cc_final: 0.7406 (ptmm) REVERT: B 86 ARG cc_start: 0.6640 (mtp180) cc_final: 0.5855 (ptt180) REVERT: B 93 ASP cc_start: 0.7319 (t0) cc_final: 0.6595 (m-30) REVERT: B 109 PHE cc_start: 0.6920 (m-10) cc_final: 0.6686 (m-80) REVERT: B 248 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7707 (mt) REVERT: B 337 ASP cc_start: 0.6773 (m-30) cc_final: 0.6507 (m-30) REVERT: B 397 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6594 (tp30) REVERT: B 398 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6368 (p0) REVERT: B 485 MET cc_start: 0.4331 (tpt) cc_final: 0.3520 (mmp) REVERT: B 490 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: B 500 MET cc_start: 0.3418 (ppp) cc_final: 0.2932 (pp-130) REVERT: C 58 ARG cc_start: 0.7396 (mmt90) cc_final: 0.7139 (mpt-90) REVERT: C 93 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: C 103 ASP cc_start: 0.7405 (t70) cc_final: 0.7006 (t0) REVERT: C 120 ILE cc_start: 0.8024 (tt) cc_final: 0.7644 (mp) REVERT: C 155 GLN cc_start: 0.7635 (mm110) cc_final: 0.7284 (mp10) REVERT: C 177 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6686 (mtm110) REVERT: C 183 ASN cc_start: 0.6798 (m-40) cc_final: 0.6281 (t160) REVERT: C 267 MET cc_start: 0.8458 (mtt) cc_final: 0.8018 (mtm) REVERT: C 288 MET cc_start: 0.7959 (tpt) cc_final: 0.7452 (tpp) REVERT: C 392 TYR cc_start: 0.7486 (m-80) cc_final: 0.7259 (m-80) REVERT: C 441 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5244 (tt0) REVERT: C 495 MET cc_start: 0.4349 (pmm) cc_final: 0.3838 (pmt) REVERT: D 56 LYS cc_start: 0.6796 (tmtt) cc_final: 0.5975 (mtmm) REVERT: D 58 ARG cc_start: 0.7580 (mtt180) cc_final: 0.7354 (ttm170) REVERT: D 59 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6934 (pt) REVERT: D 86 ARG cc_start: 0.6491 (mtp180) cc_final: 0.5751 (ptt180) REVERT: D 93 ASP cc_start: 0.7222 (t0) cc_final: 0.6531 (m-30) REVERT: D 109 PHE cc_start: 0.7217 (m-10) cc_final: 0.6962 (m-80) REVERT: D 115 LYS cc_start: 0.7937 (tppt) cc_final: 0.7725 (tppt) REVERT: D 215 ARG cc_start: 0.6514 (ptt180) cc_final: 0.6137 (mtm110) REVERT: D 248 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7356 (mt) REVERT: D 294 HIS cc_start: 0.6660 (m-70) cc_final: 0.6330 (m-70) REVERT: D 315 ARG cc_start: 0.6963 (mmm-85) cc_final: 0.6531 (mmm-85) REVERT: D 317 HIS cc_start: 0.5198 (OUTLIER) cc_final: 0.4366 (p-80) REVERT: D 330 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6278 (mm) REVERT: D 333 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5241 (tptp) REVERT: D 395 PRO cc_start: 0.7061 (Cg_endo) cc_final: 0.6777 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: D 495 MET cc_start: 0.3663 (pp-130) cc_final: 0.3305 (pp-130) REVERT: D 500 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.5001 (tmm) REVERT: D 510 MET cc_start: 0.4855 (tpp) cc_final: 0.4534 (tmm) outliers start: 121 outliers final: 62 residues processed: 290 average time/residue: 1.0495 time to fit residues: 342.2376 Evaluate side-chains 280 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 198 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 SER Chi-restraints excluded: chain A residue 227 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 310 SER Chi-restraints excluded: chain A residue 339 GLU 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 432 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 477 ASN Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 510 MET 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 141 VAL Chi-restraints excluded: chain B residue 146 SER 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 262 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 SER 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 398 ASP Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 495 MET 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 191 CYS Chi-restraints excluded: chain C residue 228 VAL 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 430 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 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 117 THR Chi-restraints excluded: chain D residue 248 ILE 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 365 SER Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 402 GLN A 403 ASN C 216 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 414 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: 0.6882 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15846 Z= 0.159 Angle : 0.575 9.979 21476 Z= 0.293 Chirality : 0.042 0.193 2422 Planarity : 0.004 0.049 2688 Dihedral : 8.858 81.409 2239 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.42 % Allowed : 28.96 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1870 helix: 0.08 (0.15), residues: 1128 sheet: -1.61 (0.56), residues: 90 loop : -0.34 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 135 HIS 0.004 0.001 HIS D 329 PHE 0.018 0.001 PHE C 409 TYR 0.025 0.001 TYR B 364 ARG 0.013 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 296 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 205 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7440 (t70) cc_final: 0.7123 (t0) REVERT: A 122 ASP cc_start: 0.7242 (p0) cc_final: 0.6943 (p0) REVERT: A 183 ASN cc_start: 0.6793 (m-40) cc_final: 0.6173 (t160) REVERT: A 267 MET cc_start: 0.8383 (mtt) cc_final: 0.8030 (mtt) REVERT: A 298 ARG cc_start: 0.7208 (ttp-170) cc_final: 0.6878 (ttt90) REVERT: A 451 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4692 (mt) REVERT: A 508 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6299 (pp20) REVERT: A 510 MET cc_start: 0.0141 (OUTLIER) cc_final: -0.0967 (ttt) REVERT: B 46 ARG cc_start: 0.5465 (ttm110) cc_final: 0.5098 (ttm-80) REVERT: B 58 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7277 (mmt90) REVERT: B 59 ILE cc_start: 0.7567 (tp) cc_final: 0.7143 (pt) REVERT: B 83 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6698 (mtm110) REVERT: B 86 ARG cc_start: 0.6450 (mtp180) cc_final: 0.5664 (ptt180) REVERT: B 93 ASP cc_start: 0.7246 (t0) cc_final: 0.6493 (m-30) REVERT: B 109 PHE cc_start: 0.6785 (m-10) cc_final: 0.6560 (m-80) REVERT: B 179 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 248 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7649 (mt) REVERT: B 307 GLN cc_start: 0.7495 (pp30) cc_final: 0.7245 (tp40) REVERT: B 336 THR cc_start: 0.7209 (m) cc_final: 0.6968 (m) REVERT: B 337 ASP cc_start: 0.6743 (m-30) cc_final: 0.6477 (m-30) REVERT: B 397 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: B 398 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6280 (p0) REVERT: B 485 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3628 (tpt) REVERT: B 497 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5994 (p0) REVERT: B 500 MET cc_start: 0.3397 (ppp) cc_final: 0.2271 (tpt) REVERT: C 93 ASP cc_start: 0.7781 (t0) cc_final: 0.7522 (m-30) REVERT: C 103 ASP cc_start: 0.7379 (t70) cc_final: 0.7013 (t0) REVERT: C 177 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6682 (mtm110) REVERT: C 182 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6681 (ttm-80) REVERT: C 183 ASN cc_start: 0.6778 (m-40) cc_final: 0.6256 (t160) REVERT: C 185 ASN cc_start: 0.6883 (m-40) cc_final: 0.6023 (t0) REVERT: C 267 MET cc_start: 0.8399 (mtt) cc_final: 0.7972 (mtm) REVERT: C 288 MET cc_start: 0.8054 (tpt) cc_final: 0.7648 (tpp) REVERT: C 372 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6064 (pp) REVERT: C 392 TYR cc_start: 0.7492 (m-80) cc_final: 0.7220 (m-80) REVERT: C 441 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5313 (tt0) REVERT: C 466 ASN cc_start: 0.5338 (OUTLIER) cc_final: 0.5107 (p0) REVERT: D 58 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7332 (mmt90) REVERT: D 59 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7059 (pt) REVERT: D 86 ARG cc_start: 0.6344 (mtp180) cc_final: 0.5633 (ptt180) REVERT: D 93 ASP cc_start: 0.7165 (t0) cc_final: 0.6453 (m-30) REVERT: D 105 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7811 (pt) REVERT: D 109 PHE cc_start: 0.7146 (m-10) cc_final: 0.6908 (m-80) REVERT: D 115 LYS cc_start: 0.7856 (tppt) cc_final: 0.7628 (tppt) REVERT: D 162 MET cc_start: 0.8415 (tpt) cc_final: 0.8110 (mmm) REVERT: D 215 ARG cc_start: 0.6496 (ptt180) cc_final: 0.6181 (mtm110) REVERT: D 248 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7163 (mm) REVERT: D 294 HIS cc_start: 0.6661 (m-70) cc_final: 0.6302 (m-70) REVERT: D 315 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.5518 (tpm170) REVERT: D 317 HIS cc_start: 0.5205 (OUTLIER) cc_final: 0.4506 (p-80) REVERT: D 330 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6323 (mm) REVERT: D 333 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5390 (tptp) REVERT: D 395 PRO cc_start: 0.7204 (Cg_endo) cc_final: 0.6931 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: D 510 MET cc_start: 0.4769 (tpp) cc_final: 0.4536 (tmm) outliers start: 91 outliers final: 42 residues processed: 274 average time/residue: 1.0953 time to fit residues: 336.1094 Evaluate side-chains 254 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 191 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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 171 VAL Chi-restraints excluded: chain A residue 217 SER 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 358 ILE Chi-restraints excluded: chain A residue 408 ASP 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 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 A residue 477 ASN Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL 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 372 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 59 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 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 367 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS B 490 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 311 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: 0.6905 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15846 Z= 0.206 Angle : 0.598 10.206 21476 Z= 0.303 Chirality : 0.042 0.163 2422 Planarity : 0.004 0.049 2688 Dihedral : 8.662 80.932 2231 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.54 % Allowed : 29.20 % Favored : 65.26 % 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: -0.22 (0.20), residues: 1870 helix: 0.17 (0.16), residues: 1128 sheet: -1.45 (0.56), residues: 90 loop : -0.24 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.019 0.001 PHE A 409 TYR 0.026 0.002 TYR B 364 ARG 0.012 0.000 ARG D 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 290 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 197 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7550 (t70) cc_final: 0.7227 (t0) REVERT: A 122 ASP cc_start: 0.7260 (p0) cc_final: 0.6943 (p0) REVERT: A 183 ASN cc_start: 0.6786 (m-40) cc_final: 0.6163 (t160) REVERT: A 267 MET cc_start: 0.8412 (mtt) cc_final: 0.7980 (mtm) REVERT: A 298 ARG cc_start: 0.7174 (ttp-170) cc_final: 0.6875 (ttt90) REVERT: A 508 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6373 (pp20) REVERT: A 510 MET cc_start: -0.0173 (OUTLIER) cc_final: -0.1265 (ttt) REVERT: B 46 ARG cc_start: 0.5431 (ttm110) cc_final: 0.5081 (ttm-80) REVERT: B 58 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7313 (tpt-90) REVERT: B 59 ILE cc_start: 0.7691 (tp) cc_final: 0.7290 (pt) REVERT: B 83 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6722 (mtm110) REVERT: B 86 ARG cc_start: 0.6410 (mtp180) cc_final: 0.5690 (ptt180) REVERT: B 93 ASP cc_start: 0.7242 (t0) cc_final: 0.6490 (m-30) REVERT: B 109 PHE cc_start: 0.6761 (m-10) cc_final: 0.6541 (m-80) REVERT: B 179 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 248 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7805 (mt) REVERT: B 307 GLN cc_start: 0.7451 (pp30) cc_final: 0.7202 (tp40) REVERT: B 337 ASP cc_start: 0.6761 (m-30) cc_final: 0.6474 (m-30) REVERT: B 397 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6562 (tp30) REVERT: B 398 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6268 (p0) REVERT: B 485 MET cc_start: 0.4290 (tpt) cc_final: 0.3759 (tpt) REVERT: B 497 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6034 (p0) REVERT: B 500 MET cc_start: 0.3352 (ppp) cc_final: 0.2259 (tpt) REVERT: C 93 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: C 103 ASP cc_start: 0.7376 (t70) cc_final: 0.7025 (t0) REVERT: C 122 ASP cc_start: 0.6489 (p0) cc_final: 0.6210 (p0) REVERT: C 155 GLN cc_start: 0.7549 (mm110) cc_final: 0.7210 (mp10) REVERT: C 182 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6655 (ttm-80) REVERT: C 183 ASN cc_start: 0.6799 (m-40) cc_final: 0.6238 (t160) REVERT: C 185 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6034 (t0) REVERT: C 267 MET cc_start: 0.8406 (mtt) cc_final: 0.8118 (mtt) REVERT: C 288 MET cc_start: 0.8061 (tpt) cc_final: 0.7634 (tpp) REVERT: C 372 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6085 (pp) REVERT: C 392 TYR cc_start: 0.7514 (m-80) cc_final: 0.7286 (m-80) REVERT: C 441 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5339 (tt0) REVERT: C 466 ASN cc_start: 0.5394 (OUTLIER) cc_final: 0.5137 (p0) REVERT: C 472 ASN cc_start: 0.5281 (OUTLIER) cc_final: 0.5062 (p0) REVERT: D 56 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5401 (mtmm) REVERT: D 59 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7011 (pt) REVERT: D 86 ARG cc_start: 0.6330 (mtp180) cc_final: 0.5555 (ptt180) REVERT: D 93 ASP cc_start: 0.7170 (t0) cc_final: 0.6457 (m-30) REVERT: D 105 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7819 (pt) REVERT: D 109 PHE cc_start: 0.7136 (m-10) cc_final: 0.6901 (m-80) REVERT: D 115 LYS cc_start: 0.7873 (tppt) cc_final: 0.7570 (tppt) REVERT: D 162 MET cc_start: 0.8425 (tpt) cc_final: 0.8101 (mmm) REVERT: D 215 ARG cc_start: 0.6487 (ptt180) cc_final: 0.6182 (mtm110) REVERT: D 248 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7530 (mm) REVERT: D 294 HIS cc_start: 0.6617 (m-70) cc_final: 0.6286 (m-70) REVERT: D 315 ARG cc_start: 0.7012 (mmm-85) cc_final: 0.5461 (tpm170) REVERT: D 317 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4508 (p-80) REVERT: D 330 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6301 (mm) REVERT: D 333 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5387 (tptp) REVERT: D 395 PRO cc_start: 0.7195 (Cg_endo) cc_final: 0.6925 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: D 500 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5181 (tmm) outliers start: 93 outliers final: 52 residues processed: 269 average time/residue: 1.0983 time to fit residues: 330.2212 Evaluate side-chains 268 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 171 VAL Chi-restraints excluded: chain A residue 217 SER 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 359 SER Chi-restraints excluded: chain A residue 408 ASP 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 453 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE 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 398 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 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 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 VAL 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 372 LEU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 171 VAL 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 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 339 GLU 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 462 LEU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS D 311 ASN D 360 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15846 Z= 0.240 Angle : 0.611 10.151 21476 Z= 0.311 Chirality : 0.043 0.204 2422 Planarity : 0.004 0.051 2688 Dihedral : 8.641 80.093 2231 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.42 % Allowed : 29.80 % Favored : 64.78 % 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: -0.21 (0.19), residues: 1870 helix: 0.16 (0.15), residues: 1128 sheet: -1.35 (0.57), residues: 90 loop : -0.20 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.014 0.001 PHE B 272 TYR 0.026 0.002 TYR B 364 ARG 0.013 0.000 ARG C 177 *********************** 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 284 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 193 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7521 (t70) cc_final: 0.7203 (t0) REVERT: A 122 ASP cc_start: 0.7269 (p0) cc_final: 0.6943 (p0) REVERT: A 183 ASN cc_start: 0.6826 (m-40) cc_final: 0.6155 (t160) REVERT: A 267 MET cc_start: 0.8447 (mtt) cc_final: 0.8002 (mtm) REVERT: A 298 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6965 (ttt90) REVERT: A 510 MET cc_start: -0.1095 (OUTLIER) cc_final: -0.2077 (ttt) REVERT: B 46 ARG cc_start: 0.5438 (ttm110) cc_final: 0.5095 (ttm-80) REVERT: B 58 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7312 (tpt-90) REVERT: B 59 ILE cc_start: 0.7650 (tp) cc_final: 0.7239 (pt) REVERT: B 83 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6737 (mtm110) REVERT: B 86 ARG cc_start: 0.6384 (mtp180) cc_final: 0.5685 (ptt180) REVERT: B 93 ASP cc_start: 0.7252 (t0) cc_final: 0.6535 (m-30) REVERT: B 109 PHE cc_start: 0.6731 (m-10) cc_final: 0.6521 (m-80) REVERT: B 164 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7066 (mtt180) REVERT: B 179 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 190 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7044 (mmm160) REVERT: B 248 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 330 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6314 (mm) REVERT: B 337 ASP cc_start: 0.6781 (m-30) cc_final: 0.6489 (m-30) REVERT: B 397 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6534 (tp30) REVERT: B 398 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6187 (p0) REVERT: B 485 MET cc_start: 0.4281 (tpt) cc_final: 0.3747 (tpt) REVERT: B 497 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6221 (p0) REVERT: B 500 MET cc_start: 0.3356 (ppp) cc_final: 0.2261 (tpt) REVERT: C 93 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: C 103 ASP cc_start: 0.7361 (t70) cc_final: 0.7020 (t0) REVERT: C 113 LEU cc_start: 0.8016 (mm) cc_final: 0.7691 (tp) REVERT: C 122 ASP cc_start: 0.6180 (p0) cc_final: 0.5941 (p0) REVERT: C 177 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6604 (mtm110) REVERT: C 183 ASN cc_start: 0.6914 (m-40) cc_final: 0.6327 (t160) REVERT: C 185 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.5975 (t0) REVERT: C 267 MET cc_start: 0.8439 (mtt) cc_final: 0.7987 (mtm) REVERT: C 288 MET cc_start: 0.8055 (tpt) cc_final: 0.7638 (tpp) REVERT: C 372 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5900 (pp) REVERT: C 392 TYR cc_start: 0.7489 (m-80) cc_final: 0.7282 (m-80) REVERT: C 441 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5246 (tt0) REVERT: C 466 ASN cc_start: 0.5392 (OUTLIER) cc_final: 0.5135 (p0) REVERT: C 495 MET cc_start: 0.4400 (pmm) cc_final: 0.3842 (pmt) REVERT: D 56 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5356 (mtmm) REVERT: D 59 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7006 (pt) REVERT: D 86 ARG cc_start: 0.6343 (mtp180) cc_final: 0.5596 (ptt180) REVERT: D 93 ASP cc_start: 0.7174 (t0) cc_final: 0.6461 (m-30) REVERT: D 105 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7734 (pt) REVERT: D 109 PHE cc_start: 0.7135 (m-10) cc_final: 0.6899 (m-80) REVERT: D 115 LYS cc_start: 0.7891 (tppt) cc_final: 0.7583 (tppt) REVERT: D 162 MET cc_start: 0.8431 (tpt) cc_final: 0.8093 (mmm) REVERT: D 215 ARG cc_start: 0.6511 (ptt180) cc_final: 0.6188 (mtm110) REVERT: D 248 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7575 (mt) REVERT: D 294 HIS cc_start: 0.6415 (m-70) cc_final: 0.6161 (m-70) REVERT: D 315 ARG cc_start: 0.6918 (mmm-85) cc_final: 0.5490 (tpm170) REVERT: D 317 HIS cc_start: 0.5207 (OUTLIER) cc_final: 0.4516 (p-80) REVERT: D 330 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6213 (mm) REVERT: D 333 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5444 (tptp) REVERT: D 395 PRO cc_start: 0.7177 (Cg_endo) cc_final: 0.6907 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: D 500 MET cc_start: 0.5561 (OUTLIER) cc_final: 0.5187 (tmm) REVERT: D 510 MET cc_start: 0.4257 (tmt) cc_final: 0.3938 (tmm) outliers start: 91 outliers final: 60 residues processed: 263 average time/residue: 1.1456 time to fit residues: 335.8634 Evaluate side-chains 273 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 189 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 217 SER 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 359 SER Chi-restraints excluded: chain A residue 408 ASP 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 453 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG 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 164 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 330 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 398 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 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 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 217 SER Chi-restraints excluded: chain C residue 228 VAL 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 372 LEU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 171 VAL 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 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 339 GLU 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 462 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 ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS D 311 ASN D 360 HIS ** 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: 0.6879 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15846 Z= 0.151 Angle : 0.576 10.169 21476 Z= 0.291 Chirality : 0.041 0.197 2422 Planarity : 0.004 0.059 2688 Dihedral : 8.248 80.922 2231 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.65 % Allowed : 30.81 % Favored : 64.54 % 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: 0.05 (0.20), residues: 1870 helix: 0.41 (0.16), residues: 1128 sheet: -1.55 (0.51), residues: 110 loop : -0.08 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 135 HIS 0.004 0.001 HIS D 329 PHE 0.022 0.001 PHE A 409 TYR 0.025 0.001 TYR B 364 ARG 0.013 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 9 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 270 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 192 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7622 (t70) cc_final: 0.7216 (t0) REVERT: A 106 MET cc_start: 0.6556 (tmm) cc_final: 0.6164 (tmm) REVERT: A 122 ASP cc_start: 0.7250 (p0) cc_final: 0.6916 (p0) REVERT: A 183 ASN cc_start: 0.6770 (m-40) cc_final: 0.6132 (t160) REVERT: A 267 MET cc_start: 0.8398 (mtt) cc_final: 0.7939 (mtm) REVERT: A 298 ARG cc_start: 0.7068 (ttp-170) cc_final: 0.6838 (ttt180) REVERT: A 510 MET cc_start: -0.0561 (OUTLIER) cc_final: -0.1552 (ttt) REVERT: B 58 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7261 (mmt90) REVERT: B 59 ILE cc_start: 0.7691 (tp) cc_final: 0.7339 (pt) REVERT: B 83 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6736 (mtm110) REVERT: B 86 ARG cc_start: 0.6242 (mtp180) cc_final: 0.5575 (ptt180) REVERT: B 93 ASP cc_start: 0.7231 (t0) cc_final: 0.6484 (m-30) REVERT: B 164 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7366 (mmt90) REVERT: B 190 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: B 248 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7856 (mt) REVERT: B 330 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6411 (mm) REVERT: B 337 ASP cc_start: 0.6723 (m-30) cc_final: 0.6458 (m-30) REVERT: B 397 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6520 (tp30) REVERT: B 398 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6115 (p0) REVERT: B 485 MET cc_start: 0.4336 (tpt) cc_final: 0.3735 (tpt) REVERT: B 497 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.6070 (p0) REVERT: B 500 MET cc_start: 0.3274 (ppp) cc_final: 0.2155 (tpt) REVERT: C 93 ASP cc_start: 0.7768 (t0) cc_final: 0.7490 (m-30) REVERT: C 103 ASP cc_start: 0.7318 (t70) cc_final: 0.7021 (t0) REVERT: C 106 MET cc_start: 0.6107 (ttm) cc_final: 0.5873 (ttp) REVERT: C 113 LEU cc_start: 0.8024 (mm) cc_final: 0.7713 (tp) REVERT: C 122 ASP cc_start: 0.6225 (p0) cc_final: 0.6021 (p0) REVERT: C 177 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6635 (mtm110) REVERT: C 183 ASN cc_start: 0.6863 (m-40) cc_final: 0.6307 (t160) REVERT: C 185 ASN cc_start: 0.6885 (OUTLIER) cc_final: 0.6076 (t0) REVERT: C 267 MET cc_start: 0.8391 (mtt) cc_final: 0.7928 (mtm) REVERT: C 288 MET cc_start: 0.8065 (tpt) cc_final: 0.7681 (tpp) REVERT: C 372 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5873 (pp) REVERT: C 392 TYR cc_start: 0.7460 (m-80) cc_final: 0.7206 (m-80) REVERT: C 441 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5231 (tt0) REVERT: C 466 ASN cc_start: 0.5355 (OUTLIER) cc_final: 0.5096 (p0) REVERT: D 56 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5356 (mtmm) REVERT: D 59 ILE cc_start: 0.7317 (tp) cc_final: 0.7082 (pt) REVERT: D 86 ARG cc_start: 0.6245 (mtp180) cc_final: 0.5528 (ptt180) REVERT: D 93 ASP cc_start: 0.7129 (t0) cc_final: 0.6419 (m-30) REVERT: D 105 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7731 (pp) REVERT: D 109 PHE cc_start: 0.7061 (m-10) cc_final: 0.6827 (m-80) REVERT: D 115 LYS cc_start: 0.7912 (tppt) cc_final: 0.7588 (tppt) REVERT: D 215 ARG cc_start: 0.6584 (ptt180) cc_final: 0.6166 (mtm110) REVERT: D 294 HIS cc_start: 0.6391 (m-70) cc_final: 0.6098 (m-70) REVERT: D 317 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.4395 (p-80) REVERT: D 330 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6278 (mm) REVERT: D 333 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5324 (tptp) REVERT: D 395 PRO cc_start: 0.7196 (Cg_endo) cc_final: 0.6932 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6889 (tp30) REVERT: D 500 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5189 (tmm) REVERT: D 510 MET cc_start: 0.4244 (tmt) cc_final: 0.3952 (tmm) outliers start: 78 outliers final: 37 residues processed: 252 average time/residue: 1.1502 time to fit residues: 323.2150 Evaluate side-chains 247 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE 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 453 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 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 243 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 170 optimal weight: 0.0050 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 360 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3700 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= 0.223 Angle : 0.610 10.282 21476 Z= 0.309 Chirality : 0.043 0.202 2422 Planarity : 0.004 0.054 2688 Dihedral : 8.233 80.074 2229 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.93 % Allowed : 31.47 % Favored : 64.60 % 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: -0.04 (0.20), residues: 1870 helix: 0.34 (0.16), residues: 1132 sheet: -1.52 (0.51), residues: 110 loop : -0.14 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.014 0.001 PHE B 109 TYR 0.024 0.002 TYR B 364 ARG 0.015 0.000 ARG B 182 ********************** REFINEMENT MACRO_CYCLE 10 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 254 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 188 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6185 (tmm) REVERT: A 122 ASP cc_start: 0.7270 (p0) cc_final: 0.6927 (p0) REVERT: A 183 ASN cc_start: 0.6770 (m-40) cc_final: 0.6116 (t160) REVERT: A 267 MET cc_start: 0.8437 (mtt) cc_final: 0.8003 (mtm) REVERT: A 298 ARG cc_start: 0.7173 (ttp-170) cc_final: 0.6926 (ttt90) REVERT: A 510 MET cc_start: -0.0711 (OUTLIER) cc_final: -0.1817 (ttt) REVERT: B 58 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7357 (tpt-90) REVERT: B 59 ILE cc_start: 0.7643 (tp) cc_final: 0.7270 (pt) REVERT: B 83 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6772 (mtm110) REVERT: B 86 ARG cc_start: 0.6264 (mtp180) cc_final: 0.5604 (ptt180) REVERT: B 93 ASP cc_start: 0.7256 (t0) cc_final: 0.6505 (m-30) REVERT: B 133 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6177 (mtm-85) REVERT: B 164 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7361 (mmt90) REVERT: B 179 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 190 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7044 (mmm160) REVERT: B 230 ASN cc_start: 0.7493 (p0) cc_final: 0.7255 (p0) REVERT: B 248 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7863 (mt) REVERT: B 330 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6270 (mm) REVERT: B 337 ASP cc_start: 0.6734 (m-30) cc_final: 0.6470 (m-30) REVERT: B 397 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6599 (tp30) REVERT: B 398 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6103 (p0) REVERT: B 485 MET cc_start: 0.4300 (tpt) cc_final: 0.3757 (tpt) REVERT: B 497 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6063 (p0) REVERT: B 500 MET cc_start: 0.3302 (ppp) cc_final: 0.2123 (tpt) REVERT: C 93 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: C 103 ASP cc_start: 0.7322 (t70) cc_final: 0.7027 (t0) REVERT: C 113 LEU cc_start: 0.8103 (mm) cc_final: 0.7793 (tp) REVERT: C 122 ASP cc_start: 0.6284 (p0) cc_final: 0.6063 (p0) REVERT: C 177 ARG cc_start: 0.7022 (mtm110) cc_final: 0.6698 (mtm110) REVERT: C 183 ASN cc_start: 0.6928 (m-40) cc_final: 0.6315 (t160) REVERT: C 185 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.5921 (t0) REVERT: C 267 MET cc_start: 0.8432 (mtt) cc_final: 0.7989 (mtm) REVERT: C 288 MET cc_start: 0.8067 (tpt) cc_final: 0.7614 (tpp) REVERT: C 372 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5965 (pp) REVERT: C 441 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5280 (tt0) REVERT: C 466 ASN cc_start: 0.5339 (OUTLIER) cc_final: 0.5085 (p0) REVERT: D 56 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5290 (mtmm) REVERT: D 59 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7050 (pt) REVERT: D 86 ARG cc_start: 0.6290 (mtp180) cc_final: 0.5541 (ptt180) REVERT: D 93 ASP cc_start: 0.7151 (t0) cc_final: 0.6434 (m-30) REVERT: D 105 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7751 (pt) REVERT: D 109 PHE cc_start: 0.7083 (m-10) cc_final: 0.6851 (m-80) REVERT: D 115 LYS cc_start: 0.7908 (tppt) cc_final: 0.7564 (tppt) REVERT: D 162 MET cc_start: 0.8408 (tpt) cc_final: 0.8092 (mmm) REVERT: D 215 ARG cc_start: 0.6640 (ptt180) cc_final: 0.6232 (mtm110) REVERT: D 248 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7553 (mt) REVERT: D 294 HIS cc_start: 0.6350 (m-70) cc_final: 0.6060 (m-70) REVERT: D 317 HIS cc_start: 0.5217 (OUTLIER) cc_final: 0.4404 (p-80) REVERT: D 330 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6176 (mm) REVERT: D 333 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5403 (tptp) REVERT: D 395 PRO cc_start: 0.7196 (Cg_endo) cc_final: 0.6924 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: D 465 MET cc_start: 0.6074 (tpp) cc_final: 0.5557 (ttt) REVERT: D 510 MET cc_start: 0.4309 (tmt) cc_final: 0.3980 (tmm) outliers start: 66 outliers final: 38 residues processed: 236 average time/residue: 1.2236 time to fit residues: 320.8015 Evaluate side-chains 249 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 187 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 171 VAL Chi-restraints excluded: chain A residue 217 SER 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 359 SER 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 453 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 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 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 243 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 ILE 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 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 311 ASN D 360 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.229736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141879 restraints weight = 16039.969| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.71 r_work: 0.3335 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3769 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= 0.205 Angle : 0.600 9.330 21476 Z= 0.305 Chirality : 0.043 0.215 2422 Planarity : 0.004 0.058 2688 Dihedral : 8.173 79.737 2229 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.53 % Allowed : 30.87 % Favored : 64.60 % 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: 0.04 (0.20), residues: 1870 helix: 0.38 (0.16), residues: 1128 sheet: -1.46 (0.51), residues: 110 loop : -0.06 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 PHE 0.022 0.001 PHE A 409 TYR 0.024 0.002 TYR B 364 ARG 0.015 0.000 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6420.57 seconds wall clock time: 114 minutes 37.96 seconds (6877.96 seconds total)