Starting phenix.real_space_refine on Tue Aug 6 04:37:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/08_2024/8wui_37855_neut.cif" } resolution = 3.4 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 10130 2.51 5 N 2498 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15340 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 8.31, per 1000 atoms: 0.54 Number of scatterers: 15340 At special positions: 0 Unit cell: (117.52, 115.44, 125.84, 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 92 16.00 P 2 15.00 O 2618 8.00 N 2498 7.00 C 10130 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.3 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 10 sheets defined 67.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 79 through 97 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.895A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.514A pdb=" N VAL B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.240A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 243 removed outlier: 3.670A pdb=" N ILE B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 287 Processing helix chain 'B' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.575A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.837A pdb=" N ILE B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.720A pdb=" N SER A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 187' Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 194 through 208 removed outlier: 4.187A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.847A pdb=" N CYS A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 330 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 97 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.894A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.515A pdb=" N VAL D 184 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.241A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.670A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.217A pdb=" N THR D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 287 Processing helix chain 'D' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE D 336 " --> pdb=" O LYS D 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 369 Processing helix chain 'D' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.576A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.838A pdb=" N ILE D 476 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 509 Processing helix chain 'D' and resid 509 through 524 Processing helix chain 'C' and resid 79 through 98 removed outlier: 3.719A pdb=" N SER C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 187' Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 194 through 208 removed outlier: 4.188A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.961A pdb=" N CYS C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 238 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR C 251 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 330 Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'C' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 418 " --> pdb=" O GLN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 541 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 137 through 139 removed outlier: 3.758A pdb=" N TYR B 137 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU B 422 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 494 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 493 " --> pdb=" O CYS B 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 441 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 471 " --> pdb=" O TYR B 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 460 through 465 removed outlier: 6.620A pdb=" N GLU B 450 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 464 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 448 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 449 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 447 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.759A pdb=" N TYR D 137 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU D 422 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 494 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 493 " --> pdb=" O CYS D 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 441 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 471 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 460 through 465 removed outlier: 6.621A pdb=" N GLU D 450 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL D 464 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 448 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 449 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB1, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 447 " --> pdb=" O ALA C 489 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2355 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: 4.12 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2302 1.30 - 1.43: 4363 1.43 - 1.56: 8865 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15694 Sorted by residual: bond pdb=" C ASN A 355 " pdb=" O ASN A 355 " ideal model delta sigma weight residual 1.235 1.310 -0.075 1.26e-02 6.30e+03 3.52e+01 bond pdb=" C ASN C 355 " pdb=" O ASN C 355 " ideal model delta sigma weight residual 1.235 1.309 -0.074 1.26e-02 6.30e+03 3.45e+01 bond pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.32e-02 5.74e+03 2.40e+01 bond pdb=" C SER C 331 " pdb=" O SER C 331 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.32e-02 5.74e+03 2.35e+01 bond pdb=" C GLN A 359 " pdb=" O GLN A 359 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 ... (remaining 15689 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.03: 101 103.03 - 110.83: 5052 110.83 - 118.62: 7273 118.62 - 126.42: 8522 126.42 - 134.21: 186 Bond angle restraints: 21134 Sorted by residual: angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 112.23 101.94 10.29 1.26e+00 6.30e-01 6.67e+01 angle pdb=" N ASN C 348 " pdb=" CA ASN C 348 " pdb=" C ASN C 348 " ideal model delta sigma weight residual 112.23 101.96 10.27 1.26e+00 6.30e-01 6.65e+01 angle pdb=" N LEU D 226 " pdb=" CA LEU D 226 " pdb=" C LEU D 226 " ideal model delta sigma weight residual 113.72 104.00 9.72 1.30e+00 5.92e-01 5.60e+01 angle pdb=" N LYS C 332 " pdb=" CA LYS C 332 " pdb=" C LYS C 332 " ideal model delta sigma weight residual 111.14 103.08 8.06 1.08e+00 8.57e-01 5.58e+01 angle pdb=" N LYS A 332 " pdb=" CA LYS A 332 " pdb=" C LYS A 332 " ideal model delta sigma weight residual 111.14 103.10 8.04 1.08e+00 8.57e-01 5.54e+01 ... (remaining 21129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7694 17.75 - 35.50: 1141 35.50 - 53.25: 408 53.25 - 71.00: 91 71.00 - 88.75: 22 Dihedral angle restraints: 9356 sinusoidal: 3958 harmonic: 5398 Sorted by residual: dihedral pdb=" CA GLU D 112 " pdb=" C GLU D 112 " pdb=" N ASN D 113 " pdb=" CA ASN D 113 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLU B 112 " pdb=" C GLU B 112 " pdb=" N ASN B 113 " pdb=" CA ASN B 113 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C CYS D 228 " pdb=" N CYS D 228 " pdb=" CA CYS D 228 " pdb=" CB CYS D 228 " ideal model delta harmonic sigma weight residual -122.60 -131.35 8.75 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 9353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1916 0.061 - 0.121: 331 0.121 - 0.182: 52 0.182 - 0.243: 22 0.243 - 0.304: 7 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 350 " pdb=" N ASN C 350 " pdb=" C ASN C 350 " pdb=" CB ASN C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2325 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C ASP C 380 " 0.094 2.00e-02 2.50e+03 pdb=" O ASP C 380 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE C 381 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 380 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASP A 380 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP A 380 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE A 381 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 270 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 271 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.054 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 198 2.59 - 3.36: 20841 3.36 - 4.13: 37714 4.13 - 4.90: 68846 Nonbonded interactions: 127610 Sorted by model distance: nonbonded pdb=" CG1 ILE A 360 " pdb=" CD1 ILE D 385 " model vdw 1.049 3.860 nonbonded pdb=" CG1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.127 3.840 nonbonded pdb=" NH2 ARG A 345 " pdb=" OE1 GLU D 374 " model vdw 1.261 3.120 nonbonded pdb=" CD1 ILE B 385 " pdb=" CG1 ILE C 360 " model vdw 1.395 3.860 nonbonded pdb=" CD1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.405 3.860 ... (remaining 127605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'B' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A)) or resid 903)) selection = (chain 'C' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'D' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A)) or resid 903)) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.300 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 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 : 0.006 0.102 15694 Z= 0.362 Angle : 0.838 17.910 21134 Z= 0.532 Chirality : 0.053 0.304 2328 Planarity : 0.006 0.100 2592 Dihedral : 19.522 88.748 5888 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 27.30 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1810 helix: -0.98 (0.16), residues: 1040 sheet: -0.97 (0.97), residues: 34 loop : -0.12 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 171 HIS 0.004 0.001 HIS C 295 PHE 0.030 0.002 PHE D 223 TYR 0.013 0.001 TYR B 237 ARG 0.004 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 235 time to evaluate : 1.518 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: B 152 ILE cc_start: 0.5216 (OUTLIER) cc_final: 0.4568 (tp) REVERT: B 377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6438 (t) REVERT: B 468 ASP cc_start: 0.5185 (t0) cc_final: 0.4528 (t0) REVERT: A 145 MET cc_start: 0.6947 (tpp) cc_final: 0.6686 (tpp) REVERT: A 351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3589 (mttp) REVERT: A 365 ARG cc_start: 0.0571 (OUTLIER) cc_final: 0.0045 (ttp-170) REVERT: D 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (t70) REVERT: D 468 ASP cc_start: 0.5363 (t0) cc_final: 0.5022 (t0) REVERT: C 183 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5435 (tt0) REVERT: C 365 ARG cc_start: 0.1331 (OUTLIER) cc_final: 0.0286 (ttp-170) REVERT: C 369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2512 (pt0) outliers start: 83 outliers final: 31 residues processed: 306 average time/residue: 0.3038 time to fit residues: 132.9134 Evaluate side-chains 227 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 GLN A 359 GLN D 295 HIS D 312 ASN D 439 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15694 Z= 0.229 Angle : 0.658 11.054 21134 Z= 0.346 Chirality : 0.044 0.172 2328 Planarity : 0.005 0.064 2592 Dihedral : 11.799 94.086 2360 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.58 % Favored : 93.98 % Rotamer: Outliers : 4.91 % Allowed : 25.64 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1810 helix: -0.26 (0.16), residues: 1074 sheet: -0.55 (1.21), residues: 20 loop : 0.06 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 92 HIS 0.004 0.001 HIS A 469 PHE 0.024 0.002 PHE D 281 TYR 0.020 0.001 TYR C 368 ARG 0.013 0.001 ARG C 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 218 time to evaluate : 1.718 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: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7061 (mmp) cc_final: 0.6283 (mmm) REVERT: B 152 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4503 (tp) REVERT: B 218 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.5650 (tt) REVERT: B 377 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6855 (t) REVERT: A 89 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 145 MET cc_start: 0.7087 (tpp) cc_final: 0.6870 (tpp) REVERT: A 369 GLU cc_start: 0.1040 (OUTLIER) cc_final: 0.0290 (pt0) REVERT: C 89 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7589 (tp) REVERT: C 205 MET cc_start: 0.6951 (ttt) cc_final: 0.6745 (ttt) REVERT: C 221 LEU cc_start: 0.7896 (mm) cc_final: 0.7540 (mt) REVERT: C 369 GLU cc_start: 0.1979 (OUTLIER) cc_final: 0.1408 (pt0) outliers start: 80 outliers final: 37 residues processed: 282 average time/residue: 0.2331 time to fit residues: 101.6327 Evaluate side-chains 222 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 HIS D 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15694 Z= 0.399 Angle : 0.711 11.839 21134 Z= 0.371 Chirality : 0.048 0.165 2328 Planarity : 0.005 0.063 2592 Dihedral : 10.562 89.889 2305 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.91 % Favored : 93.65 % Rotamer: Outliers : 6.01 % Allowed : 24.97 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1810 helix: -0.28 (0.15), residues: 1088 sheet: -0.87 (0.70), residues: 60 loop : -0.12 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 171 HIS 0.007 0.002 HIS A 295 PHE 0.020 0.002 PHE D 134 TYR 0.017 0.002 TYR C 238 ARG 0.008 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 185 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7098 (tp) REVERT: B 158 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.5988 (tppt) REVERT: B 218 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5694 (tt) REVERT: B 343 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7896 (pp) REVERT: A 89 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 306 MET cc_start: 0.8103 (mmt) cc_final: 0.7694 (mmp) REVERT: A 344 MET cc_start: 0.5671 (mmm) cc_final: 0.4482 (pmm) REVERT: A 364 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3514 (tm) REVERT: A 369 GLU cc_start: 0.1999 (OUTLIER) cc_final: 0.1750 (pt0) REVERT: D 218 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5957 (tt) REVERT: C 89 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8186 (tp) REVERT: C 205 MET cc_start: 0.7424 (ttt) cc_final: 0.7093 (ttt) REVERT: C 306 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7672 (mmp) REVERT: C 369 GLU cc_start: 0.3885 (OUTLIER) cc_final: 0.3266 (pt0) outliers start: 98 outliers final: 49 residues processed: 265 average time/residue: 0.2445 time to fit residues: 98.2640 Evaluate side-chains 227 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 167 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 84 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 164 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15694 Z= 0.187 Angle : 0.608 10.110 21134 Z= 0.313 Chirality : 0.044 0.219 2328 Planarity : 0.005 0.058 2592 Dihedral : 9.487 80.249 2300 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.25 % Favored : 94.31 % Rotamer: Outliers : 4.29 % Allowed : 26.63 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1810 helix: 0.13 (0.16), residues: 1070 sheet: -0.88 (0.72), residues: 60 loop : -0.23 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 171 HIS 0.002 0.000 HIS C 295 PHE 0.017 0.001 PHE D 281 TYR 0.015 0.001 TYR D 237 ARG 0.004 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.6911 (mmp) cc_final: 0.6337 (mmm) REVERT: B 131 LEU cc_start: 0.7444 (pp) cc_final: 0.7155 (tt) REVERT: A 89 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 126 LEU cc_start: 0.6591 (mt) cc_final: 0.6020 (mt) REVERT: A 344 MET cc_start: 0.4855 (mmm) cc_final: 0.4263 (pmm) REVERT: A 369 GLU cc_start: 0.2770 (OUTLIER) cc_final: 0.2534 (pt0) REVERT: A 393 LEU cc_start: 0.7388 (tp) cc_final: 0.6689 (pp) REVERT: D 87 MET cc_start: 0.7066 (mmp) cc_final: 0.6089 (mmm) REVERT: D 89 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.6760 (tp) REVERT: D 218 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.5141 (tt) REVERT: D 222 ILE cc_start: 0.8300 (tt) cc_final: 0.8058 (tt) REVERT: C 89 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8159 (tp) REVERT: C 205 MET cc_start: 0.7530 (ttt) cc_final: 0.7182 (ttt) REVERT: C 221 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7407 (mt) REVERT: C 322 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7198 (m-40) REVERT: C 365 ARG cc_start: 0.1782 (OUTLIER) cc_final: 0.1517 (ttp-170) REVERT: C 369 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.3716 (pt0) outliers start: 70 outliers final: 35 residues processed: 257 average time/residue: 0.2282 time to fit residues: 91.0772 Evaluate side-chains 226 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 129 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15694 Z= 0.222 Angle : 0.597 9.256 21134 Z= 0.310 Chirality : 0.044 0.222 2328 Planarity : 0.004 0.056 2592 Dihedral : 8.948 73.271 2287 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.41 % Favored : 94.14 % Rotamer: Outliers : 4.36 % Allowed : 26.93 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1810 helix: 0.23 (0.16), residues: 1068 sheet: -1.04 (0.71), residues: 60 loop : -0.23 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 171 HIS 0.003 0.001 HIS C 295 PHE 0.019 0.001 PHE D 281 TYR 0.018 0.001 TYR D 441 ARG 0.005 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 194 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7014 (mmp) cc_final: 0.6287 (mmm) REVERT: B 158 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.5803 (tttm) REVERT: B 218 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.5222 (tt) REVERT: A 89 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8298 (tp) REVERT: A 217 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6754 (mmm-85) REVERT: A 319 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7686 (tt) REVERT: A 365 ARG cc_start: 0.2466 (OUTLIER) cc_final: 0.1664 (ttp-170) REVERT: A 393 LEU cc_start: 0.7490 (tp) cc_final: 0.6867 (pp) REVERT: D 89 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.6896 (tp) REVERT: D 218 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.5454 (tt) REVERT: D 222 ILE cc_start: 0.8243 (tt) cc_final: 0.8005 (tt) REVERT: C 89 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 205 MET cc_start: 0.7467 (ttt) cc_final: 0.7139 (ttt) REVERT: C 322 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7168 (m-40) REVERT: C 398 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.4924 (mm) REVERT: C 529 ARG cc_start: 0.3076 (OUTLIER) cc_final: 0.2847 (ptt90) outliers start: 71 outliers final: 40 residues processed: 252 average time/residue: 0.2361 time to fit residues: 91.4596 Evaluate side-chains 227 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 0.0040 chunk 42 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15694 Z= 0.171 Angle : 0.591 10.943 21134 Z= 0.302 Chirality : 0.043 0.201 2328 Planarity : 0.004 0.055 2592 Dihedral : 8.153 64.891 2281 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.36 % Favored : 94.14 % Rotamer: Outliers : 4.48 % Allowed : 27.06 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1810 helix: 0.38 (0.16), residues: 1068 sheet: -1.16 (0.70), residues: 60 loop : -0.19 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 171 HIS 0.002 0.000 HIS B 363 PHE 0.021 0.001 PHE D 281 TYR 0.018 0.001 TYR D 441 ARG 0.004 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 193 time to evaluate : 1.900 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: B 87 MET cc_start: 0.7121 (mmp) cc_final: 0.6405 (mmm) REVERT: B 158 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.5906 (tttm) REVERT: A 89 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 126 LEU cc_start: 0.6554 (mt) cc_final: 0.6131 (mt) REVERT: A 365 ARG cc_start: 0.2506 (OUTLIER) cc_final: 0.1713 (ttp-170) REVERT: A 393 LEU cc_start: 0.7119 (tp) cc_final: 0.6670 (pp) REVERT: D 87 MET cc_start: 0.6887 (mmp) cc_final: 0.6138 (mmm) REVERT: D 89 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.6589 (tp) REVERT: D 218 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.5480 (tt) REVERT: D 222 ILE cc_start: 0.8242 (tt) cc_final: 0.7992 (tt) REVERT: D 346 TYR cc_start: 0.4376 (OUTLIER) cc_final: 0.4094 (t80) REVERT: C 205 MET cc_start: 0.7456 (ttt) cc_final: 0.7239 (ttp) REVERT: C 221 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 322 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7122 (m-40) REVERT: C 529 ARG cc_start: 0.3224 (OUTLIER) cc_final: 0.2946 (ptt90) outliers start: 73 outliers final: 44 residues processed: 252 average time/residue: 0.2608 time to fit residues: 100.9265 Evaluate side-chains 235 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 182 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 30.0000 chunk 19 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 173 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15694 Z= 0.189 Angle : 0.628 14.209 21134 Z= 0.316 Chirality : 0.044 0.184 2328 Planarity : 0.004 0.053 2592 Dihedral : 8.065 63.346 2281 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.52 % Favored : 93.98 % Rotamer: Outliers : 4.66 % Allowed : 27.24 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1810 helix: 0.40 (0.16), residues: 1056 sheet: -1.24 (0.71), residues: 60 loop : -0.19 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 171 HIS 0.003 0.000 HIS C 295 PHE 0.018 0.001 PHE A 539 TYR 0.016 0.001 TYR D 441 ARG 0.004 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 187 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7127 (mmp) cc_final: 0.6384 (mmm) REVERT: B 158 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5889 (tttm) REVERT: A 89 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 344 MET cc_start: 0.4260 (mmt) cc_final: 0.4002 (mmm) REVERT: A 365 ARG cc_start: 0.2522 (OUTLIER) cc_final: 0.2299 (ttp-170) REVERT: A 369 GLU cc_start: 0.3192 (OUTLIER) cc_final: 0.2151 (pp20) REVERT: A 393 LEU cc_start: 0.7081 (tp) cc_final: 0.6628 (pp) REVERT: D 87 MET cc_start: 0.6982 (mmp) cc_final: 0.6088 (mmm) REVERT: D 89 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6585 (tp) REVERT: D 218 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.5553 (tt) REVERT: D 222 ILE cc_start: 0.8261 (tt) cc_final: 0.8038 (tt) REVERT: D 346 TYR cc_start: 0.4526 (OUTLIER) cc_final: 0.4157 (t80) REVERT: C 126 LEU cc_start: 0.6643 (mt) cc_final: 0.6278 (mt) REVERT: C 205 MET cc_start: 0.7464 (ttt) cc_final: 0.7254 (ttp) REVERT: C 217 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6735 (mmm-85) REVERT: C 221 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7371 (mt) REVERT: C 306 MET cc_start: 0.7724 (mmt) cc_final: 0.7318 (mmp) REVERT: C 322 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7054 (m-40) REVERT: C 529 ARG cc_start: 0.3190 (OUTLIER) cc_final: 0.2879 (ptt90) outliers start: 76 outliers final: 53 residues processed: 251 average time/residue: 0.2458 time to fit residues: 93.7186 Evaluate side-chains 245 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 181 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15694 Z= 0.207 Angle : 0.629 12.185 21134 Z= 0.314 Chirality : 0.044 0.170 2328 Planarity : 0.004 0.053 2592 Dihedral : 8.033 61.376 2280 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.52 % Favored : 94.03 % Rotamer: Outliers : 4.91 % Allowed : 26.75 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1810 helix: 0.43 (0.16), residues: 1064 sheet: -0.87 (0.59), residues: 80 loop : -0.15 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 171 HIS 0.003 0.000 HIS C 295 PHE 0.022 0.002 PHE D 411 TYR 0.049 0.001 TYR A 82 ARG 0.005 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 188 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7158 (mmp) cc_final: 0.6379 (mmm) REVERT: B 89 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6572 (tp) REVERT: B 158 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.5889 (tttm) REVERT: B 218 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.5175 (tt) REVERT: B 346 TYR cc_start: 0.4575 (OUTLIER) cc_final: 0.4046 (t80) REVERT: A 89 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 365 ARG cc_start: 0.2231 (OUTLIER) cc_final: 0.1498 (ttp-170) REVERT: A 369 GLU cc_start: 0.3448 (OUTLIER) cc_final: 0.2567 (pp20) REVERT: A 393 LEU cc_start: 0.7040 (tp) cc_final: 0.6584 (pp) REVERT: D 87 MET cc_start: 0.7114 (mmp) cc_final: 0.6165 (mmm) REVERT: D 89 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.6564 (tp) REVERT: D 131 LEU cc_start: 0.7624 (tp) cc_final: 0.7354 (tp) REVERT: D 218 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.5599 (tt) REVERT: D 222 ILE cc_start: 0.8315 (tt) cc_final: 0.8076 (tt) REVERT: D 346 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.4086 (t80) REVERT: C 217 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6739 (mmm-85) REVERT: C 322 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7070 (m-40) REVERT: C 529 ARG cc_start: 0.3314 (OUTLIER) cc_final: 0.3015 (ptt90) outliers start: 80 outliers final: 55 residues processed: 256 average time/residue: 0.2394 time to fit residues: 93.3404 Evaluate side-chains 247 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 179 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15694 Z= 0.190 Angle : 0.636 12.095 21134 Z= 0.317 Chirality : 0.043 0.150 2328 Planarity : 0.004 0.054 2592 Dihedral : 7.935 61.559 2280 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.36 % Favored : 94.25 % Rotamer: Outliers : 4.23 % Allowed : 27.48 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1810 helix: 0.40 (0.16), residues: 1054 sheet: -0.88 (0.58), residues: 80 loop : -0.17 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 171 HIS 0.003 0.000 HIS C 295 PHE 0.023 0.001 PHE D 411 TYR 0.039 0.001 TYR C 368 ARG 0.006 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7145 (mmp) cc_final: 0.6376 (mmm) REVERT: B 89 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6536 (tp) REVERT: B 158 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.5921 (tttm) REVERT: B 202 PHE cc_start: 0.7175 (m-80) cc_final: 0.6938 (m-80) REVERT: B 346 TYR cc_start: 0.4620 (OUTLIER) cc_final: 0.4088 (t80) REVERT: A 89 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 369 GLU cc_start: 0.3523 (OUTLIER) cc_final: 0.2464 (pp20) REVERT: A 393 LEU cc_start: 0.7087 (tp) cc_final: 0.6574 (pp) REVERT: D 87 MET cc_start: 0.7083 (mmp) cc_final: 0.6137 (mmm) REVERT: D 89 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6506 (tp) REVERT: D 131 LEU cc_start: 0.7659 (tp) cc_final: 0.7401 (tp) REVERT: D 144 ARG cc_start: 0.5128 (OUTLIER) cc_final: 0.4515 (mtp85) REVERT: D 218 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.5619 (tt) REVERT: D 222 ILE cc_start: 0.8262 (tt) cc_final: 0.8003 (tt) REVERT: D 300 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (ptp90) REVERT: D 346 TYR cc_start: 0.4587 (OUTLIER) cc_final: 0.4121 (t80) REVERT: C 217 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6764 (mmm-85) REVERT: C 322 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7028 (m-40) REVERT: C 529 ARG cc_start: 0.3275 (OUTLIER) cc_final: 0.2912 (ptt90) outliers start: 69 outliers final: 49 residues processed: 246 average time/residue: 0.2524 time to fit residues: 94.1396 Evaluate side-chains 239 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 177 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15694 Z= 0.344 Angle : 0.701 11.369 21134 Z= 0.355 Chirality : 0.047 0.198 2328 Planarity : 0.004 0.055 2592 Dihedral : 8.512 59.961 2278 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.87 % Rotamer: Outliers : 3.99 % Allowed : 27.98 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1810 helix: 0.17 (0.16), residues: 1064 sheet: -0.90 (0.58), residues: 80 loop : -0.23 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 171 HIS 0.004 0.001 HIS C 230 PHE 0.022 0.002 PHE D 411 TYR 0.035 0.002 TYR C 368 ARG 0.007 0.000 ARG A 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 182 time to evaluate : 1.610 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: B 87 MET cc_start: 0.7273 (mmp) cc_final: 0.6349 (mmm) REVERT: B 89 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.6750 (tp) REVERT: B 218 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.5826 (tt) REVERT: B 432 GLU cc_start: 0.5368 (tp30) cc_final: 0.4877 (mp0) REVERT: A 89 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8278 (tp) REVERT: A 369 GLU cc_start: 0.3610 (OUTLIER) cc_final: 0.2399 (pp20) REVERT: A 393 LEU cc_start: 0.7120 (tp) cc_final: 0.6608 (pp) REVERT: D 87 MET cc_start: 0.7275 (mmp) cc_final: 0.6315 (mmm) REVERT: D 89 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.6683 (tp) REVERT: D 218 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.5643 (tt) REVERT: D 222 ILE cc_start: 0.8276 (tt) cc_final: 0.8020 (tt) REVERT: D 346 TYR cc_start: 0.4608 (OUTLIER) cc_final: 0.4152 (t80) REVERT: C 217 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7032 (mmm-85) REVERT: C 306 MET cc_start: 0.8134 (mmt) cc_final: 0.7853 (mmt) REVERT: C 322 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7050 (m-40) REVERT: C 529 ARG cc_start: 0.3507 (OUTLIER) cc_final: 0.3131 (ptt90) outliers start: 65 outliers final: 42 residues processed: 236 average time/residue: 0.2367 time to fit residues: 86.3412 Evaluate side-chains 224 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.257372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.185842 restraints weight = 19014.437| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.04 r_work: 0.3765 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15694 Z= 0.190 Angle : 0.655 11.128 21134 Z= 0.328 Chirality : 0.044 0.192 2328 Planarity : 0.004 0.055 2592 Dihedral : 8.073 58.323 2278 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.97 % Favored : 94.59 % Rotamer: Outliers : 3.13 % Allowed : 28.77 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1810 helix: 0.30 (0.16), residues: 1064 sheet: -1.25 (0.70), residues: 60 loop : -0.25 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 171 HIS 0.002 0.000 HIS B 363 PHE 0.022 0.001 PHE D 411 TYR 0.028 0.001 TYR A 82 ARG 0.014 0.000 ARG A 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.37 seconds wall clock time: 63 minutes 15.31 seconds (3795.31 seconds total)