Starting phenix.real_space_refine on Fri Feb 16 02:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7omm_12990/02_2024/7omm_12990.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7omm_12990/02_2024/7omm_12990.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/7omm_12990/02_2024/7omm_12990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7omm_12990/02_2024/7omm_12990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7omm_12990/02_2024/7omm_12990.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7omm_12990/02_2024/7omm_12990.pdb" } 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= 0.003 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 8889 2.51 5 N 2392 2.21 5 O 2669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ASP 781": "OD1" <-> "OD2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D ASP 419": "OD1" <-> "OD2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13981 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5462 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 1 Chain: "B" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3731 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 27, 'TRANS': 451} Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3768 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Time building chain proxies: 6.92, per 1000 atoms: 0.49 Number of scatterers: 13981 At special positions: 0 Unit cell: (186.329, 77.7108, 158.071, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 2669 8.00 N 2392 7.00 C 8889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 737 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 25.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.715A pdb=" N GLU B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 155 removed outlier: 4.628A pdb=" N GLU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.762A pdb=" N THR C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 149 Processing helix chain 'C' and resid 159 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.738A pdb=" N TRP C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.582A pdb=" N GLU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.037A pdb=" N THR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Proline residue: C 276 - end of helix removed outlier: 4.489A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.703A pdb=" N ILE C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 421 through 429 removed outlier: 3.715A pdb=" N GLU C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 444 Processing helix chain 'C' and resid 452 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 155 Processing helix chain 'D' and resid 165 through 173 Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 186 through 197 removed outlier: 3.694A pdb=" N GLY D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 253 through 266 removed outlier: 4.078A pdb=" N ALA D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.818A pdb=" N ILE D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 324 removed outlier: 3.772A pdb=" N LYS D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'D' and resid 353 through 362 removed outlier: 4.108A pdb=" N ASN D 357 " --> pdb=" O TRP D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.953A pdb=" N LYS D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 420 Processing helix chain 'D' and resid 427 through 437 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 456 through 476 Processing helix chain 'D' and resid 479 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.522A pdb=" N VAL A 118 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 169 removed outlier: 4.061A pdb=" N PHE A 200 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 211 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 213 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 238 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.098A pdb=" N VAL A 227 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 removed outlier: 3.644A pdb=" N PHE A 288 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.669A pdb=" N GLY A 313 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 317 through 320 removed outlier: 3.721A pdb=" N ARG A 331 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A 336 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AB2, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.772A pdb=" N ARG A 443 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 421 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 441 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 456 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 442 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 444 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=AB4, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.569A pdb=" N ASN A 504 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 513 removed outlier: 3.798A pdb=" N PHE A 594 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG A 593 " --> pdb=" O GLY A 632 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 629 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 639 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 511 through 513 removed outlier: 3.668A pdb=" N THR A 578 " --> pdb=" O GLN A 600 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 629 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 639 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 656 through 658 removed outlier: 3.671A pdb=" N VAL A 657 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 676 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 678 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP A 692 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 712 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 726 " --> pdb=" O ASN A 716 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 727 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 742 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 749 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 757 " --> pdb=" O TYR A 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.953A pdb=" N ILE B 88 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 82 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU B 90 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.739A pdb=" N LEU B 120 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.528A pdb=" N VAL C 82 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.722A pdb=" N GLY C 13 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 37 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 52 " --> pdb=" O TRP C 39 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG C 41 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 62 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.722A pdb=" N GLY C 13 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 155 removed outlier: 5.791A pdb=" N LEU C 124 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 155 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE C 126 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 125 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE C 178 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP C 127 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 180 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY C 377 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 227 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 379 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 152 through 155 removed outlier: 5.791A pdb=" N LEU C 124 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 155 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE C 126 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 125 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE C 178 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP C 127 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 180 " --> pdb=" O TRP C 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AC7, first strand: chain 'C' and resid 262 through 264 removed outlier: 8.557A pdb=" N SER C 262 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR C 342 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU C 264 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ASN C 344 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 340 " --> pdb=" O ASN C 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 284 through 287 removed outlier: 5.683A pdb=" N ALA C 285 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP C 297 " --> pdb=" O LYS C 287 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.597A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 85 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 39 through 42 removed outlier: 4.034A pdb=" N ALA D 95 " --> pdb=" O VAL D 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.192A pdb=" N LEU D 130 " --> pdb=" O THR D 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 184 through 185 removed outlier: 3.861A pdb=" N SER D 386 " --> pdb=" O TRP D 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AD5, first strand: chain 'D' and resid 347 through 350 removed outlier: 4.046A pdb=" N ASN D 350 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 372 through 373 502 hydrogen bonds defined for protein. 1347 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: 5.27 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2735 1.33 - 1.45: 3684 1.45 - 1.57: 7846 1.57 - 1.70: 2 1.70 - 1.82: 55 Bond restraints: 14322 Sorted by residual: bond pdb=" N ILE D 182 " pdb=" CA ILE D 182 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.15e-02 7.56e+03 1.92e+01 bond pdb=" N VAL D 160 " pdb=" CA VAL D 160 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.08e-02 8.57e+03 1.79e+01 bond pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.77e+01 bond pdb=" N ILE A 293 " pdb=" CA ILE A 293 " ideal model delta sigma weight residual 1.459 1.495 -0.036 9.10e-03 1.21e+04 1.58e+01 bond pdb=" N ILE D 34 " pdb=" CA ILE D 34 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.09e-02 8.42e+03 1.34e+01 ... (remaining 14317 not shown) Histogram of bond angle deviations from ideal: 96.32 - 103.99: 188 103.99 - 111.66: 5549 111.66 - 119.33: 6598 119.33 - 127.00: 6926 127.00 - 134.67: 176 Bond angle restraints: 19437 Sorted by residual: angle pdb=" N ASP D 181 " pdb=" CA ASP D 181 " pdb=" C ASP D 181 " ideal model delta sigma weight residual 111.07 121.03 -9.96 1.07e+00 8.73e-01 8.66e+01 angle pdb=" N ASP D 137 " pdb=" CA ASP D 137 " pdb=" C ASP D 137 " ideal model delta sigma weight residual 111.28 101.78 9.50 1.09e+00 8.42e-01 7.60e+01 angle pdb=" C ARG A 662 " pdb=" CA ARG A 662 " pdb=" CB ARG A 662 " ideal model delta sigma weight residual 110.44 103.83 6.61 9.00e-01 1.23e+00 5.39e+01 angle pdb=" CA ARG A 473 " pdb=" C ARG A 473 " pdb=" N PRO A 474 " ideal model delta sigma weight residual 117.67 123.91 -6.24 8.80e-01 1.29e+00 5.03e+01 angle pdb=" CA PHE D 402 " pdb=" CB PHE D 402 " pdb=" CG PHE D 402 " ideal model delta sigma weight residual 113.80 120.79 -6.99 1.00e+00 1.00e+00 4.89e+01 ... (remaining 19432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7232 17.81 - 35.62: 757 35.62 - 53.44: 311 53.44 - 71.25: 108 71.25 - 89.06: 23 Dihedral angle restraints: 8431 sinusoidal: 3300 harmonic: 5131 Sorted by residual: dihedral pdb=" CB CYS A 203 " pdb=" SG CYS A 203 " pdb=" SG CYS A 737 " pdb=" CB CYS A 737 " ideal model delta sinusoidal sigma weight residual 93.00 34.67 58.33 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CA MET A 780 " pdb=" C MET A 780 " pdb=" N ASP A 781 " pdb=" CA ASP A 781 " ideal model delta harmonic sigma weight residual 180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" N TYR D 36 " pdb=" C TYR D 36 " pdb=" CA TYR D 36 " pdb=" CB TYR D 36 " ideal model delta harmonic sigma weight residual 122.80 135.75 -12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 8428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1503 0.095 - 0.190: 407 0.190 - 0.285: 116 0.285 - 0.380: 22 0.380 - 0.475: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA TYR D 36 " pdb=" N TYR D 36 " pdb=" C TYR D 36 " pdb=" CB TYR D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB THR C 170 " pdb=" CA THR C 170 " pdb=" OG1 THR C 170 " pdb=" CG2 THR C 170 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA ILE D 389 " pdb=" N ILE D 389 " pdb=" C ILE D 389 " pdb=" CB ILE D 389 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 2049 not shown) Planarity restraints: 2546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 202 " 0.096 2.00e-02 2.50e+03 5.87e-02 6.03e+01 pdb=" CG PHE C 202 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE C 202 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE C 202 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE C 202 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE C 202 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 202 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 327 " -0.079 2.00e-02 2.50e+03 4.63e-02 4.29e+01 pdb=" CG TYR C 327 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 327 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR C 327 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 327 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 327 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR C 327 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 327 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 311 " -0.079 2.00e-02 2.50e+03 4.89e-02 4.18e+01 pdb=" CG PHE C 311 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE C 311 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE C 311 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE C 311 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 311 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 311 " -0.046 2.00e-02 2.50e+03 ... (remaining 2543 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 38 2.43 - 3.05: 8104 3.05 - 3.67: 21078 3.67 - 4.28: 31312 4.28 - 4.90: 52250 Nonbonded interactions: 112782 Sorted by model distance: nonbonded pdb=" O GLU D 401 " pdb=" OE1 GLU D 401 " model vdw 1.818 3.040 nonbonded pdb=" OD1 ASN D 296 " pdb=" N GLY D 297 " model vdw 2.224 2.520 nonbonded pdb=" OE1 GLN A 765 " pdb=" OG SER A 770 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR A 751 " pdb=" OG1 THR A 755 " model vdw 2.268 2.440 nonbonded pdb=" O TYR D 333 " pdb=" CD1 TYR D 333 " model vdw 2.276 3.340 ... (remaining 112777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 5 through 13 or resid 15 through 16 or resid 18 through 29 \ or resid 39 or resid 41 through 49 or resid 51 through 53 or resid 61 or resid \ 63 through 72 or resid 74 or resid 76 through 95 or resid 97 through 99 or resid \ 105 or resid 107 through 108 or resid 110 or resid 112 through 483)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 16 or resid 18 through 29 \ or resid 39 or resid 41 through 49 or resid 51 through 53 or resid 61 or resid \ 63 through 72 or resid 74 or resid 76 through 95 or resid 97 through 99 or resid \ 105 or resid 107 or resid 114 or resid 116 or resid 118 through 489)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 12.290 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.410 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4596 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 : 0.010 0.053 14322 Z= 0.678 Angle : 1.466 12.055 19437 Z= 1.051 Chirality : 0.097 0.475 2052 Planarity : 0.007 0.059 2546 Dihedral : 18.842 89.060 5178 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.30 % Favored : 90.19 % Rotamer: Outliers : 16.45 % Allowed : 11.92 % Favored : 71.64 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.19), residues: 1784 helix: 0.36 (0.25), residues: 410 sheet: -2.61 (0.22), residues: 479 loop : -2.36 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP C 457 HIS 0.006 0.002 HIS C 156 PHE 0.096 0.007 PHE C 202 TYR 0.079 0.004 TYR C 327 ARG 0.005 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 175 time to evaluate : 1.371 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: A 173 GLN cc_start: 0.6917 (tm-30) cc_final: 0.6203 (tm-30) REVERT: A 211 TYR cc_start: 0.8566 (p90) cc_final: 0.8285 (p90) REVERT: A 312 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 393 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 425 ASP cc_start: 0.7258 (t0) cc_final: 0.6494 (t0) REVERT: A 463 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7075 (m100) REVERT: A 473 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: A 524 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: A 565 TYR cc_start: 0.6753 (t80) cc_final: 0.6340 (t80) REVERT: A 669 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7914 (pt) REVERT: A 780 MET cc_start: 0.6148 (ppp) cc_final: 0.5371 (ppp) REVERT: B 32 TYR cc_start: 0.5960 (m-10) cc_final: 0.5743 (m-10) REVERT: B 131 GLN cc_start: 0.7887 (pp30) cc_final: 0.7652 (pp30) REVERT: C 50 TRP cc_start: 0.7684 (t60) cc_final: 0.7045 (t60) REVERT: C 55 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.7765 (m-40) REVERT: C 63 TYR cc_start: 0.6874 (m-80) cc_final: 0.6642 (m-80) REVERT: D 5 VAL cc_start: 0.3554 (OUTLIER) cc_final: 0.3243 (m) REVERT: D 22 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5861 (mmm160) REVERT: D 49 GLU cc_start: 0.2884 (OUTLIER) cc_final: 0.2657 (mp0) REVERT: D 133 TRP cc_start: 0.3770 (OUTLIER) cc_final: 0.2522 (t60) REVERT: D 149 LYS cc_start: 0.4135 (OUTLIER) cc_final: 0.3933 (mttt) REVERT: D 187 HIS cc_start: 0.1454 (OUTLIER) cc_final: 0.1153 (p90) REVERT: D 195 GLN cc_start: 0.1923 (OUTLIER) cc_final: 0.1702 (mp10) REVERT: D 467 ARG cc_start: -0.0799 (OUTLIER) cc_final: -0.1118 (ttm170) outliers start: 236 outliers final: 78 residues processed: 373 average time/residue: 0.2668 time to fit residues: 143.6764 Evaluate side-chains 219 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 126 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 GLN Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 293 LYS Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 333 TYR Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 482 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 45 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 581 GLN C 100 ASN C 318 ASN D 141 ASN D 241 ASN D 350 ASN D 357 ASN D 478 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4524 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14322 Z= 0.183 Angle : 0.652 10.307 19437 Z= 0.345 Chirality : 0.045 0.234 2052 Planarity : 0.005 0.076 2546 Dihedral : 11.591 79.021 2180 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 7.67 % Allowed : 18.95 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.19), residues: 1784 helix: 0.61 (0.24), residues: 416 sheet: -2.22 (0.23), residues: 506 loop : -2.18 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 185 HIS 0.005 0.001 HIS A 340 PHE 0.021 0.002 PHE D 190 TYR 0.031 0.001 TYR D 62 ARG 0.008 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 149 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5465 (OUTLIER) cc_final: 0.4752 (pp30) REVERT: A 155 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6969 (t80) REVERT: A 256 SER cc_start: 0.7805 (t) cc_final: 0.7361 (p) REVERT: A 312 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 425 ASP cc_start: 0.6799 (t0) cc_final: 0.6547 (t0) REVERT: A 473 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7732 (mtt-85) REVERT: A 526 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6744 (mt) REVERT: A 527 GLU cc_start: 0.8182 (mp0) cc_final: 0.7917 (mp0) REVERT: B 131 GLN cc_start: 0.7927 (pp30) cc_final: 0.7726 (pp30) REVERT: B 147 GLU cc_start: 0.7752 (tp30) cc_final: 0.7314 (tp30) REVERT: C 428 LEU cc_start: -0.0089 (OUTLIER) cc_final: -0.0380 (mp) REVERT: D 22 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5969 (mtp180) REVERT: D 35 THR cc_start: 0.5756 (OUTLIER) cc_final: 0.5459 (p) REVERT: D 357 ASN cc_start: -0.1995 (OUTLIER) cc_final: -0.2368 (t0) REVERT: D 411 GLU cc_start: 0.1601 (OUTLIER) cc_final: 0.1042 (pm20) REVERT: D 453 MET cc_start: -0.2329 (mtm) cc_final: -0.2845 (mtm) outliers start: 110 outliers final: 55 residues processed: 240 average time/residue: 0.2404 time to fit residues: 85.8079 Evaluate side-chains 190 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 125 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 160 optimal weight: 50.0000 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 40.0000 chunk 54 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 562 ASN B 53 GLN B 100 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 478 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4737 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14322 Z= 0.305 Angle : 0.716 9.165 19437 Z= 0.380 Chirality : 0.047 0.210 2052 Planarity : 0.006 0.074 2546 Dihedral : 8.712 59.887 2051 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.99 % Favored : 88.90 % Rotamer: Outliers : 7.11 % Allowed : 20.91 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.20), residues: 1784 helix: 0.73 (0.25), residues: 414 sheet: -2.35 (0.22), residues: 543 loop : -2.19 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 426 HIS 0.008 0.002 HIS D 187 PHE 0.031 0.002 PHE C 375 TYR 0.026 0.002 TYR A 565 ARG 0.006 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 121 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 173 GLN cc_start: 0.6607 (tm-30) cc_final: 0.5723 (tm-30) REVERT: A 524 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: B 51 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7636 (mm) REVERT: C 375 PHE cc_start: 0.0976 (OUTLIER) cc_final: 0.0749 (t80) REVERT: C 438 MET cc_start: 0.2581 (mmp) cc_final: 0.0990 (mmt) REVERT: D 138 LYS cc_start: 0.0224 (OUTLIER) cc_final: -0.1525 (mttt) REVERT: D 411 GLU cc_start: 0.1923 (OUTLIER) cc_final: 0.1180 (pm20) REVERT: D 418 LYS cc_start: 0.0492 (OUTLIER) cc_final: 0.0260 (pptt) outliers start: 102 outliers final: 60 residues processed: 206 average time/residue: 0.2362 time to fit residues: 73.6571 Evaluate side-chains 178 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 111 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LYS Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 107 optimal weight: 0.0270 chunk 160 optimal weight: 50.0000 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 0.0270 chunk 141 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN D 135 ASN D 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14322 Z= 0.147 Angle : 0.593 9.169 19437 Z= 0.306 Chirality : 0.043 0.187 2052 Planarity : 0.005 0.082 2546 Dihedral : 7.622 57.154 2034 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.71 % Rotamer: Outliers : 4.95 % Allowed : 22.37 % Favored : 72.68 % 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: -1.93 (0.20), residues: 1784 helix: 1.06 (0.25), residues: 411 sheet: -2.12 (0.22), residues: 535 loop : -1.85 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 138 HIS 0.004 0.001 HIS D 187 PHE 0.015 0.001 PHE D 150 TYR 0.020 0.001 TYR D 62 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 133 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5455 (OUTLIER) cc_final: 0.4716 (pp30) REVERT: A 155 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6918 (t80) REVERT: A 173 GLN cc_start: 0.6563 (tm-30) cc_final: 0.5711 (tm-30) REVERT: A 365 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6306 (t80) REVERT: A 375 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 565 TYR cc_start: 0.6995 (t80) cc_final: 0.6389 (t80) REVERT: C 438 MET cc_start: 0.2322 (mmp) cc_final: 0.0595 (mmt) REVERT: D 411 GLU cc_start: 0.1403 (OUTLIER) cc_final: 0.0929 (pm20) outliers start: 71 outliers final: 38 residues processed: 190 average time/residue: 0.2390 time to fit residues: 69.5315 Evaluate side-chains 165 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 445 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 50.0000 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN D 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14322 Z= 0.293 Angle : 0.679 9.023 19437 Z= 0.357 Chirality : 0.046 0.208 2052 Planarity : 0.005 0.064 2546 Dihedral : 7.309 56.477 2013 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.27 % Favored : 88.68 % Rotamer: Outliers : 5.85 % Allowed : 21.81 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1784 helix: 1.03 (0.26), residues: 405 sheet: -2.32 (0.22), residues: 547 loop : -1.94 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 138 HIS 0.015 0.002 HIS D 187 PHE 0.029 0.002 PHE D 381 TYR 0.022 0.002 TYR A 277 ARG 0.007 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 122 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.4964 (pp30) REVERT: A 155 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 173 GLN cc_start: 0.6634 (tm-30) cc_final: 0.5846 (tm-30) REVERT: A 211 TYR cc_start: 0.8680 (p90) cc_final: 0.8475 (p90) REVERT: A 365 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.6903 (t80) REVERT: A 375 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8006 (p0) REVERT: B 51 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7545 (mm) REVERT: B 147 GLU cc_start: 0.7818 (tp30) cc_final: 0.7355 (tp30) REVERT: B 151 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6823 (tpp80) REVERT: C 438 MET cc_start: 0.2594 (mmp) cc_final: 0.0893 (mmt) REVERT: D 113 TRP cc_start: 0.8247 (m-10) cc_final: 0.7941 (m-10) REVERT: D 411 GLU cc_start: 0.0680 (OUTLIER) cc_final: 0.0449 (pm20) REVERT: D 453 MET cc_start: -0.1369 (mtm) cc_final: -0.1789 (mtt) outliers start: 84 outliers final: 53 residues processed: 191 average time/residue: 0.2391 time to fit residues: 70.2078 Evaluate side-chains 173 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 114 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 445 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4699 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14322 Z= 0.192 Angle : 0.625 10.029 19437 Z= 0.322 Chirality : 0.044 0.182 2052 Planarity : 0.005 0.082 2546 Dihedral : 6.849 56.842 2005 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 4.46 % Allowed : 24.18 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % 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: -1.89 (0.20), residues: 1784 helix: 1.23 (0.26), residues: 400 sheet: -2.14 (0.22), residues: 539 loop : -1.83 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 138 HIS 0.005 0.001 HIS D 187 PHE 0.023 0.002 PHE D 184 TYR 0.015 0.001 TYR D 62 ARG 0.004 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 116 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.4906 (pp30) REVERT: A 173 GLN cc_start: 0.6665 (tm-30) cc_final: 0.5950 (tm-30) REVERT: A 365 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6609 (t80) REVERT: A 375 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7923 (p0) REVERT: B 51 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7496 (mm) REVERT: C 438 MET cc_start: 0.2547 (mmp) cc_final: 0.0894 (mmt) REVERT: C 453 MET cc_start: 0.2382 (mmm) cc_final: 0.1443 (mpp) REVERT: D 113 TRP cc_start: 0.8243 (m-10) cc_final: 0.7853 (m-10) REVERT: D 411 GLU cc_start: 0.1232 (OUTLIER) cc_final: 0.0619 (pm20) REVERT: D 453 MET cc_start: -0.1543 (mtm) cc_final: -0.1967 (mtt) outliers start: 64 outliers final: 47 residues processed: 167 average time/residue: 0.2424 time to fit residues: 61.6910 Evaluate side-chains 162 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 110 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 445 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 40.0000 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14322 Z= 0.231 Angle : 0.648 9.706 19437 Z= 0.336 Chirality : 0.045 0.181 2052 Planarity : 0.005 0.071 2546 Dihedral : 6.865 56.379 2005 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.15 % Favored : 88.79 % Rotamer: Outliers : 5.37 % Allowed : 23.48 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1784 helix: 1.06 (0.26), residues: 407 sheet: -2.23 (0.21), residues: 563 loop : -1.84 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 138 HIS 0.008 0.001 HIS D 187 PHE 0.024 0.002 PHE D 184 TYR 0.024 0.002 TYR A 565 ARG 0.005 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 112 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.4921 (pp30) REVERT: A 155 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: A 173 GLN cc_start: 0.6713 (tm-30) cc_final: 0.6012 (tm-30) REVERT: A 365 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6878 (t80) REVERT: A 375 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 51 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7547 (mm) REVERT: B 138 TRP cc_start: 0.7464 (m-10) cc_final: 0.7229 (m-90) REVERT: B 147 GLU cc_start: 0.7765 (tp30) cc_final: 0.7167 (tt0) REVERT: C 438 MET cc_start: 0.2642 (mmp) cc_final: 0.1007 (mmt) REVERT: C 453 MET cc_start: 0.2428 (mmm) cc_final: 0.1893 (mpp) REVERT: D 113 TRP cc_start: 0.8252 (m-10) cc_final: 0.7907 (m-10) REVERT: D 138 LYS cc_start: 0.0400 (OUTLIER) cc_final: -0.1372 (mttt) REVERT: D 165 LYS cc_start: 0.4097 (mttp) cc_final: 0.3550 (mttp) REVERT: D 184 PHE cc_start: 0.3835 (OUTLIER) cc_final: 0.3403 (m-80) REVERT: D 411 GLU cc_start: 0.0938 (OUTLIER) cc_final: 0.0528 (pm20) outliers start: 77 outliers final: 51 residues processed: 176 average time/residue: 0.2420 time to fit residues: 65.3815 Evaluate side-chains 164 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 105 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 480 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 154 optimal weight: 40.0000 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4699 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14322 Z= 0.177 Angle : 0.622 9.953 19437 Z= 0.317 Chirality : 0.044 0.182 2052 Planarity : 0.005 0.075 2546 Dihedral : 6.330 50.238 1999 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 4.88 % Allowed : 24.18 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % 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: -1.87 (0.20), residues: 1784 helix: 1.25 (0.26), residues: 405 sheet: -2.17 (0.21), residues: 575 loop : -1.75 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 138 HIS 0.006 0.001 HIS D 187 PHE 0.025 0.002 PHE D 184 TYR 0.014 0.001 TYR A 682 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 116 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5624 (OUTLIER) cc_final: 0.4892 (pp30) REVERT: A 155 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: A 173 GLN cc_start: 0.6783 (tm-30) cc_final: 0.6088 (tm-30) REVERT: A 197 GLU cc_start: 0.7179 (tp30) cc_final: 0.6634 (tm-30) REVERT: A 365 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6545 (t80) REVERT: A 375 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 527 GLU cc_start: 0.8316 (mp0) cc_final: 0.8006 (mp0) REVERT: B 51 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7480 (mm) REVERT: B 112 MET cc_start: 0.8288 (ptp) cc_final: 0.7856 (ptt) REVERT: B 147 GLU cc_start: 0.7765 (tp30) cc_final: 0.7177 (tt0) REVERT: C 438 MET cc_start: 0.2800 (mmp) cc_final: 0.1177 (mmt) REVERT: C 453 MET cc_start: 0.2402 (mmm) cc_final: 0.1966 (mpp) REVERT: D 54 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.6659 (mt) REVERT: D 113 TRP cc_start: 0.8254 (m-10) cc_final: 0.7925 (m-10) REVERT: D 165 LYS cc_start: 0.4078 (mttp) cc_final: 0.3540 (mttp) REVERT: D 184 PHE cc_start: 0.3326 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: D 411 GLU cc_start: 0.0895 (OUTLIER) cc_final: 0.0555 (pm20) outliers start: 70 outliers final: 49 residues processed: 172 average time/residue: 0.2254 time to fit residues: 60.7945 Evaluate side-chains 169 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 112 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 422 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 40.0000 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 0.0060 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4791 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14322 Z= 0.264 Angle : 0.675 10.061 19437 Z= 0.349 Chirality : 0.045 0.180 2052 Planarity : 0.005 0.068 2546 Dihedral : 6.614 50.367 1999 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.66 % Favored : 88.28 % Rotamer: Outliers : 4.67 % Allowed : 24.74 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1784 helix: 1.04 (0.26), residues: 407 sheet: -2.21 (0.21), residues: 561 loop : -1.96 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 138 HIS 0.009 0.001 HIS D 187 PHE 0.026 0.002 PHE D 184 TYR 0.028 0.002 TYR A 565 ARG 0.005 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 109 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.5009 (pp30) REVERT: A 155 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: A 173 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6164 (tm-30) REVERT: A 365 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 375 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 51 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7532 (mm) REVERT: B 138 TRP cc_start: 0.7455 (m-10) cc_final: 0.7230 (m-90) REVERT: D 54 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.6810 (mt) REVERT: D 113 TRP cc_start: 0.8316 (m-10) cc_final: 0.7953 (m-10) REVERT: D 165 LYS cc_start: 0.4230 (mttp) cc_final: 0.3741 (mttp) REVERT: D 184 PHE cc_start: 0.3983 (OUTLIER) cc_final: 0.3460 (m-80) REVERT: D 411 GLU cc_start: 0.0575 (OUTLIER) cc_final: 0.0337 (pm20) outliers start: 67 outliers final: 53 residues processed: 161 average time/residue: 0.2264 time to fit residues: 57.0167 Evaluate side-chains 166 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 105 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 175 optimal weight: 50.0000 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4801 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14322 Z= 0.273 Angle : 0.686 10.504 19437 Z= 0.354 Chirality : 0.046 0.182 2052 Planarity : 0.005 0.077 2546 Dihedral : 6.628 50.744 1999 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.48 % Favored : 89.46 % Rotamer: Outliers : 4.60 % Allowed : 24.88 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1784 helix: 1.04 (0.26), residues: 405 sheet: -2.36 (0.21), residues: 579 loop : -1.98 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 138 HIS 0.005 0.001 HIS D 187 PHE 0.024 0.002 PHE D 184 TYR 0.018 0.002 TYR A 277 ARG 0.006 0.000 ARG C 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 108 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5752 (OUTLIER) cc_final: 0.5032 (pp30) REVERT: A 155 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: A 173 GLN cc_start: 0.6905 (tm-30) cc_final: 0.6189 (tm-30) REVERT: A 365 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.6985 (t80) REVERT: A 375 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8073 (p0) REVERT: B 51 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7545 (mm) REVERT: B 138 TRP cc_start: 0.7463 (m-10) cc_final: 0.7202 (m-90) REVERT: B 147 GLU cc_start: 0.7652 (tp30) cc_final: 0.7112 (tt0) REVERT: C 438 MET cc_start: 0.2930 (mmp) cc_final: 0.1129 (mmt) REVERT: C 453 MET cc_start: 0.2628 (mmm) cc_final: 0.1514 (mpp) REVERT: D 54 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.6906 (mt) REVERT: D 113 TRP cc_start: 0.8328 (m-10) cc_final: 0.8020 (m-10) REVERT: D 165 LYS cc_start: 0.4345 (mttp) cc_final: 0.3844 (mttp) REVERT: D 184 PHE cc_start: 0.4110 (OUTLIER) cc_final: 0.3889 (m-80) REVERT: D 453 MET cc_start: -0.1853 (mtt) cc_final: -0.2114 (mtm) REVERT: D 459 MET cc_start: -0.1343 (tpt) cc_final: -0.1606 (tpt) outliers start: 66 outliers final: 56 residues processed: 163 average time/residue: 0.2240 time to fit residues: 57.4258 Evaluate side-chains 169 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 106 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.266147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.231017 restraints weight = 22648.584| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 2.34 r_work: 0.4571 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14322 Z= 0.226 Angle : 0.660 10.109 19437 Z= 0.339 Chirality : 0.045 0.181 2052 Planarity : 0.005 0.075 2546 Dihedral : 6.410 49.875 1996 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.29 % Rotamer: Outliers : 4.67 % Allowed : 25.02 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1784 helix: 1.17 (0.26), residues: 402 sheet: -2.10 (0.22), residues: 572 loop : -1.99 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 138 HIS 0.007 0.001 HIS D 187 PHE 0.025 0.002 PHE D 184 TYR 0.027 0.001 TYR A 565 ARG 0.009 0.000 ARG A 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.24 seconds wall clock time: 60 minutes 14.05 seconds (3614.05 seconds total)