Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 00:11:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm2_32598/07_2023/7wm2_32598_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 92 5.16 5 C 10072 2.51 5 N 2596 2.21 5 O 2718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D GLU 441": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 7.62, per 1000 atoms: 0.49 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: 6.41 Conformation dependent library (CDL) restraints added in 2.3 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: 1.44 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: 4.17 Time building geometry restraints manager: 6.90 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: 7990 17.87 - 35.75: 1047 35.75 - 53.62: 290 53.62 - 71.49: 66 71.49 - 89.37: 23 Dihedral angle restraints: 9416 sinusoidal: 3854 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 9413 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.470 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 39.690 Find NCS groups from input model: 1.130 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.410 ------------------------------------------------------------------------------- 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 : 18.064 89.366 5812 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 % 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 *********************** 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 : 1.830 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 outliers start: 202 outliers final: 65 residues processed: 427 average time/residue: 1.1791 time to fit residues: 558.0708 Evaluate side-chains 269 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 204 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 56 residues processed: 10 average time/residue: 0.5842 time to fit residues: 9.4274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN 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 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 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN D 126 GLN D 216 ASN D 290 ASN D 294 HIS ** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15846 Z= 0.214 Angle : 0.701 10.053 21476 Z= 0.364 Chirality : 0.045 0.220 2422 Planarity : 0.005 0.046 2688 Dihedral : 9.140 83.217 2188 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 8.52 % 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: -2.08 (0.18), residues: 1870 helix: -1.18 (0.14), residues: 1144 sheet: -2.34 (0.53), residues: 90 loop : -1.27 (0.25), residues: 636 *********************** 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 361 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 218 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 61 residues processed: 333 average time/residue: 0.9640 time to fit residues: 363.5295 Evaluate side-chains 252 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 191 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 52 residues processed: 10 average time/residue: 0.7299 time to fit residues: 10.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 0.0570 chunk 57 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 294 HIS C 216 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15846 Z= 0.213 Angle : 0.643 11.728 21476 Z= 0.328 Chirality : 0.044 0.291 2422 Planarity : 0.004 0.053 2688 Dihedral : 8.675 85.957 2188 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 7.81 % 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: -1.21 (0.19), residues: 1870 helix: -0.48 (0.15), residues: 1142 sheet: -2.01 (0.54), residues: 90 loop : -0.93 (0.24), residues: 638 *********************** 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 333 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 202 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 62 residues processed: 308 average time/residue: 1.0048 time to fit residues: 349.8698 Evaluate side-chains 256 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 52 residues processed: 10 average time/residue: 0.2781 time to fit residues: 6.5639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 87 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 15846 Z= 0.288 Angle : 0.649 9.751 21476 Z= 0.334 Chirality : 0.045 0.335 2422 Planarity : 0.004 0.045 2688 Dihedral : 8.570 87.066 2188 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 7.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1870 helix: -0.28 (0.15), residues: 1130 sheet: -2.20 (0.51), residues: 100 loop : -0.50 (0.25), residues: 640 *********************** 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 317 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 196 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 66 residues processed: 296 average time/residue: 1.0403 time to fit residues: 347.9369 Evaluate side-chains 255 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 189 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 59 residues processed: 7 average time/residue: 0.1629 time to fit residues: 4.2599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 342 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6926 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15846 Z= 0.271 Angle : 0.640 11.705 21476 Z= 0.327 Chirality : 0.045 0.302 2422 Planarity : 0.004 0.044 2688 Dihedral : 8.365 88.363 2188 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 6.97 % 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: -0.64 (0.19), residues: 1870 helix: -0.13 (0.15), residues: 1138 sheet: -2.05 (0.52), residues: 100 loop : -0.38 (0.25), residues: 632 *********************** 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 314 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 197 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 70 residues processed: 294 average time/residue: 1.0080 time to fit residues: 334.9992 Evaluate side-chains 259 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 189 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 63 residues processed: 7 average time/residue: 0.1444 time to fit residues: 4.2326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15846 Z= 0.169 Angle : 0.599 10.883 21476 Z= 0.303 Chirality : 0.042 0.218 2422 Planarity : 0.004 0.056 2688 Dihedral : 7.955 84.437 2188 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 5.84 % 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: -0.20 (0.20), residues: 1870 helix: 0.26 (0.16), residues: 1130 sheet: -1.84 (0.51), residues: 100 loop : -0.29 (0.25), residues: 640 *********************** 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 284 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 186 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 69 residues processed: 272 average time/residue: 1.0231 time to fit residues: 314.2639 Evaluate side-chains 253 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 184 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 65 residues processed: 5 average time/residue: 0.5223 time to fit residues: 5.6293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 chunk 179 optimal weight: 0.0000 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 343 GLN C 360 HIS 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: 0.6868 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 15846 Z= 0.151 Angle : 0.595 10.836 21476 Z= 0.298 Chirality : 0.042 0.258 2422 Planarity : 0.004 0.049 2688 Dihedral : 7.619 81.890 2188 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 5.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.10 (0.20), residues: 1870 helix: 0.47 (0.16), residues: 1128 sheet: -1.33 (0.56), residues: 90 loop : -0.22 (0.25), residues: 652 *********************** 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 280 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 189 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 61 residues processed: 272 average time/residue: 1.0485 time to fit residues: 322.9217 Evaluate side-chains 245 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 184 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 59 residues processed: 2 average time/residue: 0.2164 time to fit residues: 3.0870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.0370 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 403 ASN B 294 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 472 ASN D 360 HIS ** 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: 0.6879 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15846 Z= 0.168 Angle : 0.596 11.014 21476 Z= 0.298 Chirality : 0.042 0.175 2422 Planarity : 0.004 0.051 2688 Dihedral : 7.522 80.896 2188 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 4.83 % 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: 0.20 (0.20), residues: 1870 helix: 0.54 (0.16), residues: 1126 sheet: -1.25 (0.56), residues: 90 loop : -0.17 (0.25), residues: 654 *********************** 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 266 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 185 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 64 residues processed: 256 average time/residue: 1.0489 time to fit residues: 302.2305 Evaluate side-chains 245 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 181 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 61 residues processed: 4 average time/residue: 0.4479 time to fit residues: 4.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 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: 0.6865 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 15846 Z= 0.155 Angle : 0.600 12.694 21476 Z= 0.298 Chirality : 0.042 0.284 2422 Planarity : 0.004 0.058 2688 Dihedral : 7.384 79.543 2188 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 4.77 % 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: 0.31 (0.20), residues: 1870 helix: 0.65 (0.16), residues: 1126 sheet: -1.48 (0.52), residues: 100 loop : -0.07 (0.25), residues: 644 *********************** 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 263 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 183 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 58 residues processed: 255 average time/residue: 1.1249 time to fit residues: 321.0269 Evaluate side-chains 237 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 57 residues processed: 1 average time/residue: 0.1439 time to fit residues: 2.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 185 optimal weight: 0.0020 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 15846 Z= 0.223 Angle : 0.634 11.693 21476 Z= 0.316 Chirality : 0.043 0.190 2422 Planarity : 0.004 0.055 2688 Dihedral : 7.474 80.359 2188 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 4.05 % 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: 0.55 (0.16), residues: 1126 sheet: -1.15 (0.56), residues: 90 loop : -0.15 (0.25), residues: 654 ********************** 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 247 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 179 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 58 residues processed: 243 average time/residue: 1.1568 time to fit residues: 315.5919 Evaluate side-chains 235 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 177 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 55 residues processed: 3 average time/residue: 0.2263 time to fit residues: 3.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.231789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145833 restraints weight = 16111.245| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.13 r_work: 0.3279 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 15846 Z= 0.154 Angle : 0.594 11.824 21476 Z= 0.296 Chirality : 0.042 0.178 2422 Planarity : 0.004 0.061 2688 Dihedral : 7.258 78.522 2188 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 3.87 % 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: 0.32 (0.20), residues: 1870 helix: 0.64 (0.16), residues: 1138 sheet: -1.00 (0.57), residues: 90 loop : -0.16 (0.25), residues: 642 =============================================================================== Job complete usr+sys time: 6083.51 seconds wall clock time: 108 minutes 28.02 seconds (6508.02 seconds total)