Starting phenix.real_space_refine on Sun Feb 18 19:09:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsl_21893/02_2024/6wsl_21893_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4516 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 116 5.16 5 C 11490 2.51 5 N 3144 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 264": "NH1" <-> "NH2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E ASP 392": "OD1" <-> "OD2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 318": "NH1" <-> "NH2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 130": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 287": "NH1" <-> "NH2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" 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: 18204 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3378 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3370 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Chain: "C" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2026 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 230} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3378 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "F" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3370 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Chain: "G" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2026 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 230} Chain: "H" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 264 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.93, per 1000 atoms: 0.55 Number of scatterers: 18204 At special positions: 0 Unit cell: (136.95, 146.91, 120.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 12 15.00 O 3442 8.00 N 3144 7.00 C 11490 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 3.4 seconds 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 14 sheets defined 35.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 11 through 26 removed outlier: 3.779A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 removed outlier: 4.513A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 107 No H-bonds generated for 'chain 'A' and resid 104 through 107' Processing helix chain 'A' and resid 111 through 123 removed outlier: 4.981A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.484A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.635A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 230 through 238 removed outlier: 4.013A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.707A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.844A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.673A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 415 through 434 removed outlier: 3.956A pdb=" N PHE A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 421 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 433 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.660A pdb=" N VAL B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.573A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.962A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 4.291A pdb=" N THR B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 No H-bonds generated for 'chain 'B' and resid 190 through 193' Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.658A pdb=" N PHE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.028A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.603A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 3.656A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 381 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 391 " --> pdb=" O MET B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 406 through 422 removed outlier: 3.504A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.891A pdb=" N TRP C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 79 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 80 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 81 " --> pdb=" O TRP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.555A pdb=" N GLU C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 4.006A pdb=" N LEU C 156 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 removed outlier: 3.580A pdb=" N VAL C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.733A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 290 No H-bonds generated for 'chain 'C' and resid 287 through 290' Processing helix chain 'C' and resid 293 through 304 removed outlier: 4.292A pdb=" N ARG C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 removed outlier: 4.414A pdb=" N ARG D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 26 removed outlier: 3.595A pdb=" N GLN E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 removed outlier: 4.293A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 123 removed outlier: 4.839A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.552A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.626A pdb=" N LEU E 189 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 238 removed outlier: 3.721A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.982A pdb=" N CYS E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.809A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.582A pdb=" N ALA E 385 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 386 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 401 removed outlier: 4.535A pdb=" N LYS E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 removed outlier: 4.326A pdb=" N VAL E 409 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 434 removed outlier: 3.818A pdb=" N PHE E 418 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 421 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG E 422 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 425 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU E 428 " --> pdb=" O MET E 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS E 430 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 433 " --> pdb=" O LYS E 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 15 No H-bonds generated for 'chain 'F' and resid 12 through 15' Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.500A pdb=" N ASP F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.412A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 78 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 102 through 105 No H-bonds generated for 'chain 'F' and resid 102 through 105' Processing helix chain 'F' and resid 109 through 125 removed outlier: 4.000A pdb=" N VAL F 113 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP F 114 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU F 117 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP F 118 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 120 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG F 121 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS F 124 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 removed outlier: 3.783A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 removed outlier: 4.304A pdb=" N THR F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 No H-bonds generated for 'chain 'F' and resid 190 through 193' Processing helix chain 'F' and resid 205 through 210 Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.542A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 290 through 293 No H-bonds generated for 'chain 'F' and resid 290 through 293' Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 323 through 336 removed outlier: 3.799A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 391 removed outlier: 3.567A pdb=" N PHE F 378 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS F 379 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 381 " --> pdb=" O PHE F 378 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER F 382 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE F 385 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE F 389 " --> pdb=" O THR F 386 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG F 391 " --> pdb=" O MET F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 406 through 422 Processing helix chain 'G' and resid 74 through 82 removed outlier: 3.933A pdb=" N TRP G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS G 79 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS G 80 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL G 81 " --> pdb=" O TRP G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 118 through 132 removed outlier: 3.558A pdb=" N GLU G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 161 removed outlier: 3.771A pdb=" N LEU G 156 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.944A pdb=" N THR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 226 No H-bonds generated for 'chain 'G' and resid 224 through 226' Processing helix chain 'G' and resid 236 through 248 removed outlier: 3.672A pdb=" N PHE G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY G 248 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 304 removed outlier: 3.769A pdb=" N LEU G 294 " --> pdb=" O PHE G 290 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG G 302 " --> pdb=" O ALA G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 50 removed outlier: 4.457A pdb=" N ARG H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE H 39 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 6 through 9 Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.667A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 201 through 204 removed outlier: 7.528A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.528A pdb=" N SER A 379 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 320 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.736A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS B 129 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL B 5 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLN B 131 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N ILE B 7 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N PHE B 133 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.662A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 214 through 218 removed outlier: 3.574A pdb=" N GLY C 216 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 256 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR C 196 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU C 254 " --> pdb=" O TYR C 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 6 through 9 Processing sheet with id= I, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= J, first strand: chain 'E' and resid 134 through 137 removed outlier: 7.010A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= L, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.749A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYS F 129 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL F 5 " --> pdb=" O CYS F 129 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLN F 131 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 12.487A pdb=" N ILE F 7 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N PHE F 133 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 163 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU F 135 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.612A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 214 through 218 removed outlier: 3.776A pdb=" N GLY G 216 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 192 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 256 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR G 196 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU G 254 " --> pdb=" O TYR G 196 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3096 1.32 - 1.46: 7168 1.46 - 1.60: 8158 1.60 - 1.74: 12 1.74 - 1.89: 192 Bond restraints: 18626 Sorted by residual: bond pdb=" C2' G2P F 501 " pdb=" C3' G2P F 501 " ideal model delta sigma weight residual 1.528 1.232 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.232 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4' G2P B 501 " pdb=" C5' G2P B 501 " ideal model delta sigma weight residual 1.518 1.388 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C4' G2P F 501 " pdb=" C5' G2P F 501 " ideal model delta sigma weight residual 1.518 1.389 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1' G2P F 501 " pdb=" C2' G2P F 501 " ideal model delta sigma weight residual 1.537 1.656 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 18621 not shown) Histogram of bond angle deviations from ideal: 98.52 - 107.80: 865 107.80 - 117.07: 12105 117.07 - 126.35: 12000 126.35 - 135.63: 286 135.63 - 144.90: 2 Bond angle restraints: 25258 Sorted by residual: angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 106.50 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C4 G2P F 501 " ideal model delta sigma weight residual 125.17 108.06 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 144.90 -16.98 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C8 G2P F 501 " ideal model delta sigma weight residual 127.92 143.41 -15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C PRO G 117 " pdb=" N VAL G 118 " pdb=" CA VAL G 118 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 ... (remaining 25253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.48: 10670 29.48 - 58.95: 468 58.95 - 88.43: 41 88.43 - 117.91: 3 117.91 - 147.39: 4 Dihedral angle restraints: 11186 sinusoidal: 4588 harmonic: 6598 Sorted by residual: dihedral pdb=" CA VAL B 286 " pdb=" C VAL B 286 " pdb=" N PRO B 287 " pdb=" CA PRO B 287 " ideal model delta harmonic sigma weight residual 180.00 139.75 40.25 0 5.00e+00 4.00e-02 6.48e+01 dihedral pdb=" CA VAL F 286 " pdb=" C VAL F 286 " pdb=" N PRO F 287 " pdb=" CA PRO F 287 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.83e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -42.79 147.39 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 11183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2157 0.059 - 0.118: 532 0.118 - 0.177: 51 0.177 - 0.235: 4 0.235 - 0.294: 2 Chirality restraints: 2746 Sorted by residual: chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2743 not shown) Planarity restraints: 3278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 286 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO B 287 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 286 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO F 287 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 287 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 287 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 165 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO G 166 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " -0.033 5.00e-02 4.00e+02 ... (remaining 3275 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5211 2.79 - 3.32: 15650 3.32 - 3.85: 30661 3.85 - 4.37: 35397 4.37 - 4.90: 59508 Nonbonded interactions: 146427 Sorted by model distance: nonbonded pdb=" OG SER B 278 " pdb=" OE1 GLN B 279 " model vdw 2.264 2.440 nonbonded pdb=" O SER B 382 " pdb=" OG1 THR B 386 " model vdw 2.283 2.440 nonbonded pdb=" OG SER G 269 " pdb=" OE1 GLU G 271 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR E 292 " pdb=" OH TYR E 319 " model vdw 2.306 2.440 nonbonded pdb=" O2' G2P B 501 " pdb=" O3' G2P B 501 " model vdw 2.307 2.432 ... (remaining 146422 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 6.780 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 48.850 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.007 0.296 18626 Z= 0.452 Angle : 0.823 18.673 25258 Z= 0.424 Chirality : 0.049 0.294 2746 Planarity : 0.006 0.088 3278 Dihedral : 15.871 147.387 6942 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 8.98 % Allowed : 12.24 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -5.33 (0.13), residues: 2258 helix: -4.51 (0.07), residues: 834 sheet: -3.27 (0.27), residues: 294 loop : -2.73 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 275 HIS 0.004 0.001 HIS E 139 PHE 0.018 0.002 PHE E 255 TYR 0.016 0.002 TYR B 310 ARG 0.008 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 461 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9261 (mm) REVERT: A 90 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6827 (tp30) REVERT: A 97 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7868 (tp30) REVERT: A 155 GLU cc_start: 0.8774 (tt0) cc_final: 0.8566 (tt0) REVERT: A 192 HIS cc_start: 0.8092 (t-90) cc_final: 0.7696 (t-90) REVERT: A 258 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (t0) REVERT: A 316 CYS cc_start: 0.8138 (t) cc_final: 0.7705 (t) REVERT: A 326 LYS cc_start: 0.8419 (tptp) cc_final: 0.8018 (mttt) REVERT: A 392 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 396 ASP cc_start: 0.8783 (t70) cc_final: 0.8458 (t0) REVERT: A 432 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 31 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8355 (t70) REVERT: B 68 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 147 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: B 166 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 179 VAL cc_start: 0.9269 (t) cc_final: 0.9041 (p) REVERT: B 190 HIS cc_start: 0.8257 (t-90) cc_final: 0.8012 (t70) REVERT: B 280 GLN cc_start: 0.7704 (pt0) cc_final: 0.7339 (pm20) REVERT: B 363 MET cc_start: 0.7474 (mmt) cc_final: 0.6973 (mmt) REVERT: B 377 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9085 (tm) REVERT: C 145 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8060 (mmtt) REVERT: C 160 MET cc_start: 0.8096 (mmt) cc_final: 0.7701 (mmm) REVERT: C 180 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7529 (p) REVERT: C 183 MET cc_start: 0.7814 (mtm) cc_final: 0.7538 (mpp) REVERT: C 187 GLU cc_start: 0.7559 (tt0) cc_final: 0.7346 (mp0) REVERT: C 215 TYR cc_start: 0.5042 (m-80) cc_final: 0.3638 (m-10) REVERT: C 275 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.5900 (m100) REVERT: C 291 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6576 (mtt90) REVERT: C 295 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: C 296 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8204 (tmm-80) REVERT: C 297 HIS cc_start: 0.5962 (t70) cc_final: 0.5548 (t70) REVERT: E 60 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8489 (tttm) REVERT: E 90 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7096 (mm-30) REVERT: E 171 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8203 (mp) REVERT: E 192 HIS cc_start: 0.8173 (t-90) cc_final: 0.7971 (t-90) REVERT: E 216 ASN cc_start: 0.9032 (m-40) cc_final: 0.8620 (m-40) REVERT: E 255 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8206 (t80) REVERT: E 316 CYS cc_start: 0.8053 (t) cc_final: 0.7068 (t) REVERT: E 411 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8099 (mm-30) REVERT: F 3 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5689 (mm-30) REVERT: F 19 LYS cc_start: 0.8522 (tppt) cc_final: 0.8204 (tptm) REVERT: F 108 GLU cc_start: 0.8686 (tp30) cc_final: 0.8445 (tp30) REVERT: F 121 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8394 (mtm-85) REVERT: F 127 CYS cc_start: 0.6774 (m) cc_final: 0.5912 (m) REVERT: F 131 GLN cc_start: 0.8500 (tp40) cc_final: 0.7970 (tp40) REVERT: F 164 MET cc_start: 0.8509 (tpp) cc_final: 0.7877 (tpp) REVERT: F 166 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8514 (p) REVERT: F 190 HIS cc_start: 0.8234 (t-90) cc_final: 0.6657 (t70) REVERT: F 198 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: F 200 TYR cc_start: 0.8791 (m-80) cc_final: 0.8285 (m-80) REVERT: F 202 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (mp) REVERT: F 364 SER cc_start: 0.8735 (p) cc_final: 0.8532 (m) REVERT: G 145 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8051 (mmtm) REVERT: G 160 MET cc_start: 0.7979 (mmt) cc_final: 0.7742 (mmm) REVERT: G 180 THR cc_start: 0.8592 (p) cc_final: 0.7766 (p) REVERT: G 183 MET cc_start: 0.7704 (mtm) cc_final: 0.7464 (mpp) REVERT: G 202 PHE cc_start: 0.4974 (m-80) cc_final: 0.4647 (t80) REVERT: G 214 ARG cc_start: 0.7622 (mmt-90) cc_final: 0.7380 (mmp80) REVERT: G 215 TYR cc_start: 0.4647 (m-80) cc_final: 0.4193 (m-10) REVERT: G 234 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7457 (mmm160) REVERT: G 249 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7055 (ptp-170) REVERT: G 301 MET cc_start: 0.7315 (mtm) cc_final: 0.6946 (mmm) REVERT: H 44 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7960 (tpm170) outliers start: 176 outliers final: 67 residues processed: 591 average time/residue: 0.3350 time to fit residues: 285.0008 Evaluate side-chains 391 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 305 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 15 GLN A 28 HIS A 88 HIS ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 186 ASN A 197 HIS A 266 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 94 GLN B 134 GLN B 190 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 334 GLN B 426 GLN C 80 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 186 ASN E 197 HIS E 249 ASN E 256 GLN E 309 HIS E 329 ASN F 94 GLN F 134 GLN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 334 GLN F 370 ASN G 80 HIS G 181 ASN G 277 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18626 Z= 0.291 Angle : 0.627 8.615 25258 Z= 0.321 Chirality : 0.044 0.190 2746 Planarity : 0.005 0.064 3278 Dihedral : 11.807 146.493 2726 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.92 % Allowed : 18.67 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -4.28 (0.15), residues: 2258 helix: -3.24 (0.12), residues: 850 sheet: -3.08 (0.27), residues: 310 loop : -2.32 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 74 HIS 0.007 0.001 HIS G 204 PHE 0.015 0.001 PHE A 255 TYR 0.021 0.001 TYR A 357 ARG 0.005 0.000 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 320 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6881 (mm-30) REVERT: A 155 GLU cc_start: 0.8793 (tt0) cc_final: 0.8519 (tt0) REVERT: A 258 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8682 (t0) REVERT: A 392 ASP cc_start: 0.8332 (t70) cc_final: 0.7851 (t0) REVERT: A 396 ASP cc_start: 0.8833 (t70) cc_final: 0.8528 (t0) REVERT: A 432 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 31 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8306 (t70) REVERT: B 164 MET cc_start: 0.7943 (tpp) cc_final: 0.7720 (tpp) REVERT: B 166 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 191 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7563 (tp-100) REVERT: B 267 MET cc_start: 0.8394 (ptp) cc_final: 0.8177 (ptp) REVERT: B 280 GLN cc_start: 0.7713 (pt0) cc_final: 0.7332 (pm20) REVERT: B 287 PRO cc_start: 0.8051 (Cg_endo) cc_final: 0.7721 (Cg_exo) REVERT: B 363 MET cc_start: 0.7344 (mmt) cc_final: 0.7034 (mmt) REVERT: B 377 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9008 (tm) REVERT: B 405 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 412 GLU cc_start: 0.8220 (tp30) cc_final: 0.7860 (tp30) REVERT: C 123 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8051 (tm-30) REVERT: C 160 MET cc_start: 0.7818 (mmt) cc_final: 0.7515 (mmm) REVERT: C 180 THR cc_start: 0.8370 (p) cc_final: 0.7547 (p) REVERT: C 183 MET cc_start: 0.7984 (mtm) cc_final: 0.7585 (mpp) REVERT: C 215 TYR cc_start: 0.3998 (m-80) cc_final: 0.3627 (m-10) REVERT: C 275 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.5776 (m100) REVERT: C 290 PHE cc_start: 0.5172 (t80) cc_final: 0.4967 (m-10) REVERT: C 291 ARG cc_start: 0.7193 (mtp-110) cc_final: 0.6582 (mtt90) REVERT: E 77 GLU cc_start: 0.8475 (tp30) cc_final: 0.7992 (tp30) REVERT: E 90 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7205 (mm-30) REVERT: E 216 ASN cc_start: 0.9085 (m-40) cc_final: 0.8739 (m-40) REVERT: E 255 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8131 (t80) REVERT: E 411 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8062 (mm-30) REVERT: F 19 LYS cc_start: 0.8667 (tppt) cc_final: 0.8245 (tptp) REVERT: F 125 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8033 (mm-30) REVERT: F 127 CYS cc_start: 0.6614 (m) cc_final: 0.5657 (m) REVERT: F 131 GLN cc_start: 0.8433 (tp40) cc_final: 0.8038 (tp40) REVERT: F 164 MET cc_start: 0.8428 (tpp) cc_final: 0.7847 (tpp) REVERT: F 166 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8440 (p) REVERT: F 190 HIS cc_start: 0.7435 (t-90) cc_final: 0.6976 (t70) REVERT: F 191 GLN cc_start: 0.7973 (mm110) cc_final: 0.7494 (mm110) REVERT: F 198 GLU cc_start: 0.8189 (pt0) cc_final: 0.7704 (pt0) REVERT: F 200 TYR cc_start: 0.8857 (m-80) cc_final: 0.8282 (m-80) REVERT: F 202 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8523 (mp) REVERT: F 252 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8359 (mmtp) REVERT: F 320 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7755 (tpp80) REVERT: F 362 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (ttpp) REVERT: G 145 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7978 (mttm) REVERT: G 180 THR cc_start: 0.8507 (p) cc_final: 0.7837 (p) REVERT: G 183 MET cc_start: 0.7736 (mtm) cc_final: 0.7525 (mpp) REVERT: G 202 PHE cc_start: 0.4845 (m-80) cc_final: 0.4398 (t80) REVERT: G 220 MET cc_start: 0.4624 (ptp) cc_final: 0.4360 (ptp) REVERT: G 234 ARG cc_start: 0.7668 (tpt90) cc_final: 0.7456 (mmm160) REVERT: G 249 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7382 (ptp90) REVERT: G 292 LYS cc_start: 0.7586 (mttp) cc_final: 0.7372 (pttt) REVERT: G 296 ARG cc_start: 0.6290 (tmm160) cc_final: 0.5062 (mmm160) REVERT: G 301 MET cc_start: 0.7126 (mtm) cc_final: 0.6856 (mmm) REVERT: H 44 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7939 (tpm170) outliers start: 116 outliers final: 75 residues processed: 413 average time/residue: 0.2947 time to fit residues: 184.6310 Evaluate side-chains 358 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 272 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain G residue 289 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 356 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 165 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 329 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 18626 Z= 0.325 Angle : 0.605 6.939 25258 Z= 0.309 Chirality : 0.045 0.158 2746 Planarity : 0.005 0.101 3278 Dihedral : 11.103 146.712 2676 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.99 % Allowed : 19.08 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -3.61 (0.16), residues: 2258 helix: -2.48 (0.15), residues: 846 sheet: -3.03 (0.26), residues: 310 loop : -2.01 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.009 0.001 HIS C 297 PHE 0.012 0.001 PHE B 367 TYR 0.018 0.001 TYR A 357 ARG 0.005 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 290 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6950 (mm-30) REVERT: A 114 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 155 GLU cc_start: 0.8807 (tt0) cc_final: 0.8560 (tt0) REVERT: A 258 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8674 (t0) REVERT: A 392 ASP cc_start: 0.8390 (t70) cc_final: 0.7943 (t0) REVERT: A 396 ASP cc_start: 0.8852 (t70) cc_final: 0.8555 (t0) REVERT: A 432 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8210 (t80) REVERT: B 50 TYR cc_start: 0.8593 (m-80) cc_final: 0.8145 (m-10) REVERT: B 131 GLN cc_start: 0.8402 (tp-100) cc_final: 0.8176 (tp40) REVERT: B 166 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 197 ASP cc_start: 0.8521 (p0) cc_final: 0.8311 (p0) REVERT: B 280 GLN cc_start: 0.7752 (pt0) cc_final: 0.7366 (pm20) REVERT: B 322 SER cc_start: 0.9119 (m) cc_final: 0.8752 (t) REVERT: B 363 MET cc_start: 0.7382 (mmt) cc_final: 0.7117 (mmt) REVERT: B 377 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9109 (tm) REVERT: B 412 GLU cc_start: 0.8363 (tp30) cc_final: 0.8032 (tp30) REVERT: C 123 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8079 (tm-30) REVERT: C 160 MET cc_start: 0.7896 (mmt) cc_final: 0.7607 (mmm) REVERT: C 180 THR cc_start: 0.8350 (p) cc_final: 0.7538 (p) REVERT: C 183 MET cc_start: 0.7979 (mtm) cc_final: 0.7523 (mpp) REVERT: C 275 TRP cc_start: 0.6815 (OUTLIER) cc_final: 0.5877 (m100) REVERT: C 290 PHE cc_start: 0.5300 (t80) cc_final: 0.5046 (m-10) REVERT: C 291 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6641 (mtt90) REVERT: E 77 GLU cc_start: 0.8459 (tp30) cc_final: 0.8046 (tp30) REVERT: E 90 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 216 ASN cc_start: 0.9099 (m-40) cc_final: 0.8793 (m-40) REVERT: E 255 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8189 (t80) REVERT: E 411 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8130 (mm-30) REVERT: F 12 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7900 (t) REVERT: F 19 LYS cc_start: 0.8816 (tppt) cc_final: 0.8510 (tptp) REVERT: F 125 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8101 (mm-30) REVERT: F 131 GLN cc_start: 0.8480 (tp40) cc_final: 0.8032 (tp40) REVERT: F 164 MET cc_start: 0.8488 (tpp) cc_final: 0.7887 (tpp) REVERT: F 166 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8465 (p) REVERT: F 191 GLN cc_start: 0.8067 (mm110) cc_final: 0.7746 (mm110) REVERT: F 198 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: F 200 TYR cc_start: 0.8859 (m-80) cc_final: 0.8558 (m-80) REVERT: F 202 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (mp) REVERT: F 252 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8122 (mmtp) REVERT: F 362 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8692 (ttpp) REVERT: F 363 MET cc_start: 0.7609 (mtp) cc_final: 0.7340 (mtm) REVERT: G 145 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7924 (mttm) REVERT: G 180 THR cc_start: 0.8383 (p) cc_final: 0.7659 (p) REVERT: G 183 MET cc_start: 0.7734 (mtm) cc_final: 0.7432 (mpp) REVERT: G 202 PHE cc_start: 0.4775 (m-80) cc_final: 0.4242 (t80) REVERT: G 214 ARG cc_start: 0.7128 (mmp80) cc_final: 0.6789 (tpp-160) REVERT: G 228 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6555 (p90) REVERT: G 234 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7401 (mmm160) REVERT: G 249 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7419 (ptp90) REVERT: G 292 LYS cc_start: 0.7563 (mttp) cc_final: 0.7200 (ptpt) REVERT: G 296 ARG cc_start: 0.6477 (tmm160) cc_final: 0.5306 (tpt90) REVERT: G 301 MET cc_start: 0.6977 (mtm) cc_final: 0.6736 (mmm) outliers start: 137 outliers final: 95 residues processed: 399 average time/residue: 0.2852 time to fit residues: 174.9022 Evaluate side-chains 377 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 268 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 50.0000 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 50.0000 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 50.0000 chunk 216 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 3.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18626 Z= 0.229 Angle : 0.557 8.942 25258 Z= 0.280 Chirality : 0.043 0.272 2746 Planarity : 0.004 0.098 3278 Dihedral : 10.721 146.359 2666 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.09 % Allowed : 19.18 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -3.19 (0.17), residues: 2258 helix: -1.99 (0.16), residues: 864 sheet: -2.86 (0.26), residues: 310 loop : -1.87 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 344 HIS 0.009 0.001 HIS G 204 PHE 0.012 0.001 PHE A 255 TYR 0.017 0.001 TYR F 50 ARG 0.005 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 300 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 114 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 155 GLU cc_start: 0.8805 (tt0) cc_final: 0.8572 (tt0) REVERT: A 258 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8671 (t0) REVERT: A 392 ASP cc_start: 0.8373 (t70) cc_final: 0.7908 (t0) REVERT: A 396 ASP cc_start: 0.8812 (t70) cc_final: 0.8520 (t0) REVERT: A 432 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8205 (t80) REVERT: B 12 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7711 (t) REVERT: B 19 LYS cc_start: 0.8628 (tppt) cc_final: 0.8307 (tptp) REVERT: B 50 TYR cc_start: 0.8511 (m-80) cc_final: 0.8094 (m-10) REVERT: B 164 MET cc_start: 0.7970 (tpp) cc_final: 0.7741 (tpp) REVERT: B 166 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8258 (p) REVERT: B 191 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7821 (tp-100) REVERT: B 267 MET cc_start: 0.8262 (ptp) cc_final: 0.8047 (ptp) REVERT: B 280 GLN cc_start: 0.7665 (pt0) cc_final: 0.7282 (pm20) REVERT: B 299 MET cc_start: 0.9076 (mmt) cc_final: 0.8685 (mmt) REVERT: B 322 SER cc_start: 0.9093 (m) cc_final: 0.8689 (t) REVERT: B 412 GLU cc_start: 0.8428 (tp30) cc_final: 0.8104 (tp30) REVERT: C 123 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8115 (tm-30) REVERT: C 160 MET cc_start: 0.7869 (mmt) cc_final: 0.7618 (mmm) REVERT: C 180 THR cc_start: 0.8332 (p) cc_final: 0.7554 (p) REVERT: C 183 MET cc_start: 0.7965 (mtm) cc_final: 0.7464 (mpp) REVERT: C 275 TRP cc_start: 0.6801 (OUTLIER) cc_final: 0.5938 (m100) REVERT: C 290 PHE cc_start: 0.5327 (t80) cc_final: 0.5042 (m-10) REVERT: C 291 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.6669 (mtt90) REVERT: D 44 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7838 (tpm170) REVERT: E 90 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 114 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8689 (tp) REVERT: E 216 ASN cc_start: 0.9072 (m-40) cc_final: 0.8854 (m-40) REVERT: E 255 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8233 (t80) REVERT: E 316 CYS cc_start: 0.8073 (t) cc_final: 0.7444 (t) REVERT: F 12 CYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7927 (t) REVERT: F 19 LYS cc_start: 0.8770 (tppt) cc_final: 0.8536 (tptp) REVERT: F 50 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: F 125 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8145 (mm-30) REVERT: F 131 GLN cc_start: 0.8362 (tp40) cc_final: 0.7932 (tp40) REVERT: F 164 MET cc_start: 0.8440 (tpp) cc_final: 0.7899 (tpp) REVERT: F 166 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8466 (p) REVERT: F 198 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: F 200 TYR cc_start: 0.8823 (m-80) cc_final: 0.8262 (m-80) REVERT: F 202 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8597 (mp) REVERT: F 252 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8134 (mmtp) REVERT: F 320 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7457 (tpp80) REVERT: F 362 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8662 (ttpp) REVERT: F 363 MET cc_start: 0.7610 (mtp) cc_final: 0.7372 (mtm) REVERT: G 134 TYR cc_start: 0.5527 (t80) cc_final: 0.5164 (t80) REVERT: G 145 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7882 (mttm) REVERT: G 180 THR cc_start: 0.8390 (p) cc_final: 0.7604 (p) REVERT: G 183 MET cc_start: 0.7759 (mtm) cc_final: 0.7428 (mpp) REVERT: G 202 PHE cc_start: 0.4731 (m-80) cc_final: 0.4472 (m-10) REVERT: G 214 ARG cc_start: 0.7153 (mmp80) cc_final: 0.6897 (tpp-160) REVERT: G 228 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6568 (p90) REVERT: G 234 ARG cc_start: 0.7665 (tpt90) cc_final: 0.7391 (mmm160) REVERT: G 249 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7412 (ptp90) REVERT: G 292 LYS cc_start: 0.7669 (mttp) cc_final: 0.7372 (pttt) outliers start: 139 outliers final: 95 residues processed: 409 average time/residue: 0.2928 time to fit residues: 182.7749 Evaluate side-chains 381 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 270 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain G residue 289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 184 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18626 Z= 0.204 Angle : 0.552 10.179 25258 Z= 0.275 Chirality : 0.043 0.238 2746 Planarity : 0.004 0.093 3278 Dihedral : 10.473 146.258 2653 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.58 % Allowed : 21.07 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -2.80 (0.17), residues: 2258 helix: -1.61 (0.16), residues: 866 sheet: -2.68 (0.26), residues: 312 loop : -1.69 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.004 0.001 HIS G 204 PHE 0.017 0.001 PHE A 255 TYR 0.017 0.001 TYR A 24 ARG 0.008 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 292 time to evaluate : 2.121 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 90 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6953 (mm-30) REVERT: A 155 GLU cc_start: 0.8800 (tt0) cc_final: 0.8559 (tt0) REVERT: A 258 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8595 (t0) REVERT: A 392 ASP cc_start: 0.8367 (t70) cc_final: 0.7887 (t0) REVERT: A 396 ASP cc_start: 0.8784 (t70) cc_final: 0.8497 (t0) REVERT: A 432 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 4 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8846 (pt) REVERT: B 12 CYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7814 (t) REVERT: B 50 TYR cc_start: 0.8475 (m-80) cc_final: 0.8028 (m-10) REVERT: B 166 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 191 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7847 (tp-100) REVERT: B 267 MET cc_start: 0.8222 (ptp) cc_final: 0.7971 (ptp) REVERT: B 280 GLN cc_start: 0.7703 (pt0) cc_final: 0.7323 (pm20) REVERT: B 299 MET cc_start: 0.9080 (mmt) cc_final: 0.8591 (mmt) REVERT: B 322 SER cc_start: 0.9071 (m) cc_final: 0.8675 (t) REVERT: B 412 GLU cc_start: 0.8450 (tp30) cc_final: 0.8204 (tp30) REVERT: C 123 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8131 (tm-30) REVERT: C 160 MET cc_start: 0.7879 (mmt) cc_final: 0.7619 (mmm) REVERT: C 180 THR cc_start: 0.8337 (p) cc_final: 0.7561 (p) REVERT: C 183 MET cc_start: 0.7960 (mtm) cc_final: 0.7460 (mpp) REVERT: C 275 TRP cc_start: 0.6860 (OUTLIER) cc_final: 0.5974 (m100) REVERT: C 291 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6642 (mtt90) REVERT: D 44 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7870 (tpm170) REVERT: E 62 VAL cc_start: 0.9282 (t) cc_final: 0.9008 (m) REVERT: E 90 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7210 (mm-30) REVERT: E 255 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8254 (t80) REVERT: F 12 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8038 (t) REVERT: F 19 LYS cc_start: 0.8797 (tppt) cc_final: 0.8556 (tptp) REVERT: F 50 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: F 73 MET cc_start: 0.8209 (mmm) cc_final: 0.7906 (mmm) REVERT: F 164 MET cc_start: 0.8449 (tpp) cc_final: 0.7930 (tpp) REVERT: F 166 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8483 (p) REVERT: F 198 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: F 200 TYR cc_start: 0.8788 (m-80) cc_final: 0.8214 (m-80) REVERT: F 202 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8618 (mp) REVERT: F 252 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8092 (mmtp) REVERT: F 320 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7476 (tpp80) REVERT: F 362 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8669 (ttpp) REVERT: F 363 MET cc_start: 0.7563 (mtp) cc_final: 0.7157 (mtm) REVERT: F 364 SER cc_start: 0.8792 (p) cc_final: 0.8568 (m) REVERT: G 145 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7874 (mttm) REVERT: G 180 THR cc_start: 0.8378 (p) cc_final: 0.7605 (p) REVERT: G 183 MET cc_start: 0.7759 (mtm) cc_final: 0.7444 (mpp) REVERT: G 202 PHE cc_start: 0.4696 (m-80) cc_final: 0.4470 (m-10) REVERT: G 214 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6913 (tpp-160) REVERT: G 228 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6068 (p90) REVERT: G 234 ARG cc_start: 0.7672 (tpt90) cc_final: 0.7407 (mmm160) REVERT: G 249 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7415 (ptp90) REVERT: G 292 LYS cc_start: 0.7673 (mttp) cc_final: 0.7380 (pttt) outliers start: 129 outliers final: 93 residues processed: 392 average time/residue: 0.2902 time to fit residues: 174.4380 Evaluate side-chains 383 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 275 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18626 Z= 0.262 Angle : 0.578 8.967 25258 Z= 0.287 Chirality : 0.044 0.251 2746 Planarity : 0.004 0.102 3278 Dihedral : 10.440 145.878 2648 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.14 % Allowed : 21.02 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2258 helix: -1.40 (0.17), residues: 860 sheet: -2.60 (0.27), residues: 312 loop : -1.61 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 388 HIS 0.004 0.001 HIS F 190 PHE 0.016 0.001 PHE A 255 TYR 0.014 0.001 TYR F 50 ARG 0.003 0.000 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 288 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7243 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 114 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 155 GLU cc_start: 0.8782 (tt0) cc_final: 0.8545 (tt0) REVERT: A 258 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8613 (t0) REVERT: A 392 ASP cc_start: 0.8385 (t70) cc_final: 0.7902 (t0) REVERT: A 396 ASP cc_start: 0.8801 (t70) cc_final: 0.8521 (t0) REVERT: A 432 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8151 (t80) REVERT: B 12 CYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7908 (t) REVERT: B 19 LYS cc_start: 0.8653 (tppt) cc_final: 0.8339 (tptp) REVERT: B 65 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7940 (mt) REVERT: B 166 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 191 GLN cc_start: 0.8375 (tp-100) cc_final: 0.7876 (tp40) REVERT: B 280 GLN cc_start: 0.7721 (pt0) cc_final: 0.7265 (pm20) REVERT: B 299 MET cc_start: 0.9084 (mmt) cc_final: 0.8683 (mmt) REVERT: B 322 SER cc_start: 0.9088 (m) cc_final: 0.8691 (t) REVERT: B 412 GLU cc_start: 0.8470 (tp30) cc_final: 0.8221 (tp30) REVERT: C 123 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8126 (tm-30) REVERT: C 160 MET cc_start: 0.7838 (mmt) cc_final: 0.7583 (mmm) REVERT: C 180 THR cc_start: 0.8269 (p) cc_final: 0.7488 (p) REVERT: C 183 MET cc_start: 0.7968 (mtm) cc_final: 0.7426 (mpp) REVERT: C 275 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.5987 (m100) REVERT: C 291 ARG cc_start: 0.7235 (mtp-110) cc_final: 0.6655 (mtt90) REVERT: D 44 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7889 (tpm170) REVERT: E 62 VAL cc_start: 0.9299 (t) cc_final: 0.9021 (m) REVERT: E 90 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7248 (mm-30) REVERT: E 255 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8235 (t80) REVERT: E 432 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7971 (t80) REVERT: F 12 CYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8083 (t) REVERT: F 19 LYS cc_start: 0.8855 (tppt) cc_final: 0.8563 (tptp) REVERT: F 50 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: F 131 GLN cc_start: 0.8301 (tp40) cc_final: 0.7958 (tp40) REVERT: F 164 MET cc_start: 0.8482 (tpp) cc_final: 0.7950 (tpp) REVERT: F 166 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8583 (p) REVERT: F 198 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: F 200 TYR cc_start: 0.8824 (m-80) cc_final: 0.8246 (m-80) REVERT: F 202 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8618 (mp) REVERT: F 252 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8113 (mmtp) REVERT: F 320 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7507 (tpp80) REVERT: F 336 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8702 (tmmt) REVERT: F 362 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8656 (ttpp) REVERT: F 363 MET cc_start: 0.7478 (mtp) cc_final: 0.7225 (mtm) REVERT: G 145 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7841 (mttm) REVERT: G 180 THR cc_start: 0.8313 (p) cc_final: 0.7570 (p) REVERT: G 183 MET cc_start: 0.7767 (mtm) cc_final: 0.7456 (mpp) REVERT: G 202 PHE cc_start: 0.4631 (m-80) cc_final: 0.4397 (m-10) REVERT: G 214 ARG cc_start: 0.7191 (mmp80) cc_final: 0.6916 (tpp-160) REVERT: G 220 MET cc_start: 0.5696 (ptt) cc_final: 0.5045 (ttt) REVERT: G 228 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6068 (p90) REVERT: G 234 ARG cc_start: 0.7675 (tpt90) cc_final: 0.7400 (mmm160) REVERT: G 288 ASP cc_start: 0.7326 (t70) cc_final: 0.6850 (t0) REVERT: G 292 LYS cc_start: 0.7694 (mttp) cc_final: 0.7460 (pttt) outliers start: 140 outliers final: 98 residues processed: 398 average time/residue: 0.2918 time to fit residues: 178.0270 Evaluate side-chains 387 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 272 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18626 Z= 0.169 Angle : 0.550 11.441 25258 Z= 0.270 Chirality : 0.043 0.320 2746 Planarity : 0.004 0.095 3278 Dihedral : 10.179 146.143 2648 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.92 % Allowed : 22.65 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -2.37 (0.17), residues: 2258 helix: -1.17 (0.17), residues: 870 sheet: -2.43 (0.27), residues: 312 loop : -1.53 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.003 0.001 HIS A 192 PHE 0.017 0.001 PHE A 255 TYR 0.013 0.001 TYR A 24 ARG 0.003 0.000 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 305 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9271 (mm) REVERT: A 114 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 155 GLU cc_start: 0.8793 (tt0) cc_final: 0.8538 (tt0) REVERT: A 320 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8623 (ptm-80) REVERT: A 377 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7686 (tmm) REVERT: A 392 ASP cc_start: 0.8339 (t70) cc_final: 0.7852 (t0) REVERT: A 396 ASP cc_start: 0.8760 (t70) cc_final: 0.8405 (t0) REVERT: A 432 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 12 CYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 19 LYS cc_start: 0.8587 (tppt) cc_final: 0.8272 (tptm) REVERT: B 50 TYR cc_start: 0.8591 (m-80) cc_final: 0.8211 (m-10) REVERT: B 99 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: B 166 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8266 (p) REVERT: B 191 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7800 (tp40) REVERT: B 197 ASP cc_start: 0.8335 (p0) cc_final: 0.8103 (p0) REVERT: B 267 MET cc_start: 0.8243 (ptp) cc_final: 0.7991 (ptp) REVERT: B 280 GLN cc_start: 0.7680 (pt0) cc_final: 0.7326 (pm20) REVERT: B 299 MET cc_start: 0.9044 (mmt) cc_final: 0.8562 (mmt) REVERT: B 322 SER cc_start: 0.9058 (m) cc_final: 0.8649 (t) REVERT: C 77 MET cc_start: 0.7464 (tpt) cc_final: 0.7211 (mmm) REVERT: C 123 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8118 (tm-30) REVERT: C 160 MET cc_start: 0.7804 (mmt) cc_final: 0.7564 (mmm) REVERT: C 180 THR cc_start: 0.8386 (p) cc_final: 0.7613 (p) REVERT: C 183 MET cc_start: 0.7960 (mtm) cc_final: 0.7424 (mpp) REVERT: C 275 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.6000 (m100) REVERT: C 288 ASP cc_start: 0.7087 (t70) cc_final: 0.6834 (p0) REVERT: C 291 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6648 (mtt90) REVERT: D 44 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7899 (tpm170) REVERT: E 62 VAL cc_start: 0.9310 (t) cc_final: 0.9088 (m) REVERT: E 90 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7230 (mm-30) REVERT: E 255 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8214 (t80) REVERT: F 12 CYS cc_start: 0.8465 (t) cc_final: 0.8056 (t) REVERT: F 19 LYS cc_start: 0.8823 (tppt) cc_final: 0.8547 (tptp) REVERT: F 125 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8273 (mm-30) REVERT: F 198 GLU cc_start: 0.8170 (pt0) cc_final: 0.7613 (pt0) REVERT: F 200 TYR cc_start: 0.8772 (m-80) cc_final: 0.8195 (m-80) REVERT: F 202 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (mp) REVERT: F 252 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8091 (mmtp) REVERT: F 320 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7456 (tpp80) REVERT: F 321 MET cc_start: 0.8351 (mmp) cc_final: 0.8031 (mmp) REVERT: F 336 LYS cc_start: 0.8947 (tmmt) cc_final: 0.8683 (tmmt) REVERT: F 362 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8662 (ttpp) REVERT: F 363 MET cc_start: 0.7438 (mtp) cc_final: 0.7148 (mtm) REVERT: G 145 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7863 (mttm) REVERT: G 155 ASP cc_start: 0.7596 (m-30) cc_final: 0.7340 (m-30) REVERT: G 180 THR cc_start: 0.8294 (p) cc_final: 0.7529 (p) REVERT: G 183 MET cc_start: 0.7752 (mtm) cc_final: 0.7454 (mpp) REVERT: G 214 ARG cc_start: 0.7181 (mmp80) cc_final: 0.6955 (tpp-160) REVERT: G 228 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.5849 (p90) REVERT: G 234 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7430 (mmm160) REVERT: G 288 ASP cc_start: 0.7282 (t70) cc_final: 0.6825 (t0) REVERT: G 292 LYS cc_start: 0.7776 (mttp) cc_final: 0.7546 (pttt) outliers start: 116 outliers final: 82 residues processed: 396 average time/residue: 0.2912 time to fit residues: 176.9487 Evaluate side-chains 377 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 281 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18626 Z= 0.199 Angle : 0.569 11.744 25258 Z= 0.279 Chirality : 0.043 0.266 2746 Planarity : 0.004 0.106 3278 Dihedral : 10.022 145.658 2636 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.77 % Allowed : 22.70 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -2.29 (0.18), residues: 2258 helix: -1.06 (0.17), residues: 876 sheet: -2.30 (0.28), residues: 312 loop : -1.56 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 74 HIS 0.004 0.001 HIS B 6 PHE 0.016 0.001 PHE A 255 TYR 0.019 0.001 TYR A 357 ARG 0.003 0.000 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 287 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 155 GLU cc_start: 0.8778 (tt0) cc_final: 0.8538 (tt0) REVERT: A 320 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8666 (ptm-80) REVERT: A 377 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 392 ASP cc_start: 0.8328 (t70) cc_final: 0.7850 (t0) REVERT: A 396 ASP cc_start: 0.8769 (t70) cc_final: 0.8490 (t0) REVERT: A 398 MET cc_start: 0.8926 (ttm) cc_final: 0.8305 (ttm) REVERT: A 432 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 12 CYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7935 (t) REVERT: B 19 LYS cc_start: 0.8608 (tppt) cc_final: 0.8299 (tptm) REVERT: B 50 TYR cc_start: 0.8586 (m-80) cc_final: 0.8201 (m-10) REVERT: B 166 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 191 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7893 (tp40) REVERT: B 197 ASP cc_start: 0.8318 (p0) cc_final: 0.8053 (p0) REVERT: B 267 MET cc_start: 0.8231 (ptp) cc_final: 0.7977 (ptp) REVERT: B 280 GLN cc_start: 0.7727 (pt0) cc_final: 0.7305 (pm20) REVERT: B 299 MET cc_start: 0.9038 (mmt) cc_final: 0.8537 (mmt) REVERT: B 322 SER cc_start: 0.9063 (m) cc_final: 0.8701 (t) REVERT: C 123 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8094 (tm-30) REVERT: C 160 MET cc_start: 0.7803 (mmt) cc_final: 0.7566 (mmm) REVERT: C 180 THR cc_start: 0.8323 (p) cc_final: 0.7511 (p) REVERT: C 183 MET cc_start: 0.7951 (mtm) cc_final: 0.7393 (mpp) REVERT: C 275 TRP cc_start: 0.6904 (OUTLIER) cc_final: 0.6046 (m100) REVERT: C 288 ASP cc_start: 0.7085 (t70) cc_final: 0.6836 (p0) REVERT: C 291 ARG cc_start: 0.7231 (mtp-110) cc_final: 0.6644 (mtt90) REVERT: D 44 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7837 (tpm170) REVERT: E 90 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7220 (mm-30) REVERT: E 255 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8249 (t80) REVERT: E 432 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7926 (t80) REVERT: F 12 CYS cc_start: 0.8494 (t) cc_final: 0.8061 (t) REVERT: F 19 LYS cc_start: 0.8803 (tppt) cc_final: 0.8526 (tptp) REVERT: F 50 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8331 (m-10) REVERT: F 125 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8295 (mm-30) REVERT: F 131 GLN cc_start: 0.8063 (tp40) cc_final: 0.7679 (tp40) REVERT: F 198 GLU cc_start: 0.8139 (pt0) cc_final: 0.7585 (pt0) REVERT: F 200 TYR cc_start: 0.8762 (m-80) cc_final: 0.8210 (m-80) REVERT: F 202 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8577 (mp) REVERT: F 252 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8119 (mmtp) REVERT: F 320 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7521 (tpp80) REVERT: F 336 LYS cc_start: 0.8923 (tmmt) cc_final: 0.8689 (tmmt) REVERT: F 362 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8664 (ttpp) REVERT: F 363 MET cc_start: 0.7451 (mtp) cc_final: 0.7209 (mtm) REVERT: G 145 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7898 (mttm) REVERT: G 155 ASP cc_start: 0.7504 (m-30) cc_final: 0.7261 (m-30) REVERT: G 180 THR cc_start: 0.8242 (p) cc_final: 0.7514 (p) REVERT: G 183 MET cc_start: 0.7775 (mtm) cc_final: 0.7463 (mpp) REVERT: G 202 PHE cc_start: 0.4942 (m-80) cc_final: 0.4396 (m-10) REVERT: G 214 ARG cc_start: 0.7183 (mmp80) cc_final: 0.6952 (tpp-160) REVERT: G 228 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.5878 (p90) REVERT: G 288 ASP cc_start: 0.7288 (t70) cc_final: 0.6845 (t0) REVERT: G 292 LYS cc_start: 0.7787 (mttp) cc_final: 0.7575 (pttt) outliers start: 113 outliers final: 86 residues processed: 380 average time/residue: 0.2902 time to fit residues: 168.1643 Evaluate side-chains 377 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 277 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 190 optimal weight: 0.4980 chunk 200 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 131 GLN B 165 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18626 Z= 0.159 Angle : 0.567 10.807 25258 Z= 0.275 Chirality : 0.043 0.280 2746 Planarity : 0.004 0.105 3278 Dihedral : 9.799 145.330 2633 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.10 % Allowed : 23.67 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -2.07 (0.18), residues: 2258 helix: -0.90 (0.17), residues: 866 sheet: -2.14 (0.29), residues: 302 loop : -1.44 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 74 HIS 0.002 0.000 HIS C 136 PHE 0.016 0.001 PHE A 255 TYR 0.015 0.001 TYR A 24 ARG 0.003 0.000 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 307 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9099 (t) cc_final: 0.8707 (m) REVERT: A 114 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 155 GLU cc_start: 0.8788 (tt0) cc_final: 0.8514 (tt0) REVERT: A 357 TYR cc_start: 0.8117 (m-80) cc_final: 0.7879 (m-80) REVERT: A 396 ASP cc_start: 0.8745 (t70) cc_final: 0.8392 (t0) REVERT: A 398 MET cc_start: 0.8911 (ttm) cc_final: 0.8300 (ttm) REVERT: A 432 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 12 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8092 (t) REVERT: B 19 LYS cc_start: 0.8575 (tppt) cc_final: 0.8238 (tptm) REVERT: B 50 TYR cc_start: 0.8558 (m-80) cc_final: 0.8263 (m-80) REVERT: B 166 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 191 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7862 (tp40) REVERT: B 197 ASP cc_start: 0.8274 (p0) cc_final: 0.8021 (p0) REVERT: B 267 MET cc_start: 0.8166 (ptp) cc_final: 0.7945 (ptp) REVERT: B 280 GLN cc_start: 0.7765 (pt0) cc_final: 0.7263 (pm20) REVERT: B 299 MET cc_start: 0.8993 (mmt) cc_final: 0.8521 (mmt) REVERT: B 322 SER cc_start: 0.9051 (m) cc_final: 0.8634 (t) REVERT: C 123 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8073 (tm-30) REVERT: C 160 MET cc_start: 0.7802 (mmt) cc_final: 0.7569 (mmm) REVERT: C 180 THR cc_start: 0.8351 (p) cc_final: 0.7522 (p) REVERT: C 183 MET cc_start: 0.7942 (mtm) cc_final: 0.7407 (mpp) REVERT: C 275 TRP cc_start: 0.6861 (OUTLIER) cc_final: 0.5956 (m100) REVERT: C 288 ASP cc_start: 0.7166 (t70) cc_final: 0.6871 (p0) REVERT: C 291 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6631 (mtt90) REVERT: D 44 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7819 (tpm170) REVERT: E 50 ASN cc_start: 0.8165 (m-40) cc_final: 0.7572 (m-40) REVERT: E 90 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7209 (mm-30) REVERT: E 255 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8254 (t80) REVERT: F 12 CYS cc_start: 0.8483 (t) cc_final: 0.8039 (t) REVERT: F 19 LYS cc_start: 0.8794 (tppt) cc_final: 0.8534 (tptp) REVERT: F 22 GLU cc_start: 0.7946 (tp30) cc_final: 0.7714 (tp30) REVERT: F 125 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8299 (mm-30) REVERT: F 131 GLN cc_start: 0.7877 (tp40) cc_final: 0.7490 (tp40) REVERT: F 198 GLU cc_start: 0.8129 (pt0) cc_final: 0.7635 (pt0) REVERT: F 200 TYR cc_start: 0.8707 (m-80) cc_final: 0.8314 (m-80) REVERT: F 252 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8113 (mmtp) REVERT: F 320 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7493 (tpp80) REVERT: F 321 MET cc_start: 0.8269 (mmp) cc_final: 0.7994 (mmp) REVERT: F 336 LYS cc_start: 0.8935 (tmmt) cc_final: 0.8715 (tmmt) REVERT: F 359 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7398 (mtm110) REVERT: F 362 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8661 (ttpp) REVERT: F 363 MET cc_start: 0.7258 (mtp) cc_final: 0.7054 (mtm) REVERT: F 405 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7530 (tm-30) REVERT: G 145 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7900 (mttm) REVERT: G 155 ASP cc_start: 0.7541 (m-30) cc_final: 0.7273 (m-30) REVERT: G 180 THR cc_start: 0.8257 (p) cc_final: 0.7507 (p) REVERT: G 183 MET cc_start: 0.7768 (mtm) cc_final: 0.7468 (mpp) REVERT: G 228 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.5862 (p90) REVERT: G 288 ASP cc_start: 0.7299 (t70) cc_final: 0.6845 (t0) REVERT: G 292 LYS cc_start: 0.7849 (mttp) cc_final: 0.7552 (ptpt) outliers start: 100 outliers final: 75 residues processed: 386 average time/residue: 0.3024 time to fit residues: 177.2979 Evaluate side-chains 362 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 278 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain G residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 40.0000 chunk 129 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 134 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18626 Z= 0.182 Angle : 0.597 13.877 25258 Z= 0.287 Chirality : 0.044 0.370 2746 Planarity : 0.005 0.113 3278 Dihedral : 9.628 144.822 2627 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.44 % Allowed : 24.29 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -2.03 (0.18), residues: 2258 helix: -0.83 (0.18), residues: 868 sheet: -2.11 (0.29), residues: 312 loop : -1.43 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 74 HIS 0.012 0.001 HIS G 297 PHE 0.015 0.001 PHE A 255 TYR 0.015 0.001 TYR A 24 ARG 0.005 0.000 ARG E 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 289 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9101 (t) cc_final: 0.8713 (m) REVERT: A 114 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 155 GLU cc_start: 0.8776 (tt0) cc_final: 0.8550 (tt0) REVERT: A 156 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.8043 (mtp85) REVERT: A 357 TYR cc_start: 0.8187 (m-80) cc_final: 0.7946 (m-80) REVERT: A 396 ASP cc_start: 0.8754 (t70) cc_final: 0.8478 (t0) REVERT: A 398 MET cc_start: 0.8920 (ttm) cc_final: 0.8330 (ttm) REVERT: A 432 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 12 CYS cc_start: 0.8635 (t) cc_final: 0.8080 (t) REVERT: B 166 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 191 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7870 (tp40) REVERT: B 197 ASP cc_start: 0.8294 (p0) cc_final: 0.8079 (p0) REVERT: B 267 MET cc_start: 0.8180 (ptp) cc_final: 0.7920 (ptp) REVERT: B 280 GLN cc_start: 0.7804 (pt0) cc_final: 0.7308 (pm20) REVERT: B 299 MET cc_start: 0.8986 (mmt) cc_final: 0.8529 (mmt) REVERT: B 322 SER cc_start: 0.9049 (m) cc_final: 0.8636 (t) REVERT: C 123 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8071 (tm-30) REVERT: C 160 MET cc_start: 0.7810 (mmt) cc_final: 0.7577 (mmm) REVERT: C 180 THR cc_start: 0.8324 (p) cc_final: 0.7482 (p) REVERT: C 183 MET cc_start: 0.7947 (mtm) cc_final: 0.7387 (mpp) REVERT: C 275 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6179 (m100) REVERT: C 288 ASP cc_start: 0.7159 (t70) cc_final: 0.6885 (p0) REVERT: C 291 ARG cc_start: 0.7218 (mtp-110) cc_final: 0.6695 (mpt-90) REVERT: E 90 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 255 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8345 (t80) REVERT: F 12 CYS cc_start: 0.8514 (t) cc_final: 0.8068 (t) REVERT: F 19 LYS cc_start: 0.8795 (tppt) cc_final: 0.8549 (tptp) REVERT: F 22 GLU cc_start: 0.7941 (tp30) cc_final: 0.7726 (tp30) REVERT: F 125 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8292 (mm-30) REVERT: F 131 GLN cc_start: 0.7848 (tp40) cc_final: 0.7468 (tp40) REVERT: F 164 MET cc_start: 0.8081 (tpp) cc_final: 0.7701 (tpp) REVERT: F 198 GLU cc_start: 0.8142 (pt0) cc_final: 0.7577 (pt0) REVERT: F 200 TYR cc_start: 0.8756 (m-80) cc_final: 0.8335 (m-80) REVERT: F 252 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8108 (mmtp) REVERT: F 320 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7537 (tpp80) REVERT: F 321 MET cc_start: 0.8241 (mmp) cc_final: 0.7965 (mmp) REVERT: F 336 LYS cc_start: 0.8946 (tmmt) cc_final: 0.8717 (tmmt) REVERT: F 362 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (ttpp) REVERT: F 363 MET cc_start: 0.7283 (mtp) cc_final: 0.7063 (mtm) REVERT: F 405 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7533 (tm-30) REVERT: G 145 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7895 (mttm) REVERT: G 155 ASP cc_start: 0.7516 (m-30) cc_final: 0.6882 (t70) REVERT: G 180 THR cc_start: 0.8289 (p) cc_final: 0.7541 (p) REVERT: G 183 MET cc_start: 0.7774 (mtm) cc_final: 0.7492 (mpp) REVERT: G 228 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6280 (p90) REVERT: G 288 ASP cc_start: 0.7306 (t70) cc_final: 0.6852 (t0) REVERT: G 292 LYS cc_start: 0.7927 (mttp) cc_final: 0.7623 (ptpt) outliers start: 87 outliers final: 76 residues processed: 363 average time/residue: 0.2942 time to fit residues: 164.9300 Evaluate side-chains 361 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 277 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 0.0040 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 HIS ** 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 = 0.4341 r_free = 0.4341 target = 0.135013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.093475 restraints weight = 33821.050| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.34 r_work: 0.3490 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18626 Z= 0.150 Angle : 0.599 13.034 25258 Z= 0.286 Chirality : 0.043 0.362 2746 Planarity : 0.004 0.109 3278 Dihedral : 9.434 144.614 2626 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.11 % Allowed : 25.56 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.94 (0.18), residues: 2258 helix: -0.78 (0.18), residues: 878 sheet: -1.91 (0.30), residues: 302 loop : -1.43 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 74 HIS 0.011 0.001 HIS G 297 PHE 0.014 0.001 PHE E 52 TYR 0.017 0.001 TYR A 24 ARG 0.005 0.000 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.49 seconds wall clock time: 80 minutes 54.39 seconds (4854.39 seconds total)