Starting phenix.real_space_refine on Mon Jul 28 09:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.map" model { file = "/net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmq_9849/07_2025/6jmq_9849.cif" } resolution = 3.31 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= 0.000 sd= 0.003 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 35 5.16 5 C 6468 2.51 5 N 1606 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3101 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3520 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 212 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 3, 'TRANS': 26} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 140 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 340 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 834 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 486 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 119} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.86, per 1000 atoms: 0.69 Number of scatterers: 9950 At special positions: 0 Unit cell: (130.634, 83.979, 154.628, 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 35 16.00 O 1841 8.00 N 1606 7.00 C 6468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 704 " - " ASN B 424 " " NAG B 705 " - " ASN B 506 " " NAG B 706 " - " ASN B 365 " " NAG E 1 " - " ASN B 381 " TRANS " UNK C 31 " - " THR C 30 " " UNK C 50 " - " GLY C 49 " " UNK C 98 " - " ARG C 97 " " UNK D 24 " - " CYS D 23 " " UNK D 95 " - " CYS D 94 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 42.4% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.738A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.060A pdb=" N ILE A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.060A pdb=" N GLY A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 113 removed outlier: 3.606A pdb=" N VAL A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.110A pdb=" N TYR A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.600A pdb=" N ILE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.513A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 189 removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.595A pdb=" N ALA A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.514A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.708A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.014A pdb=" N SER A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 265 removed outlier: 3.668A pdb=" N THR A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.535A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.029A pdb=" N VAL A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.547A pdb=" N ASP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.600A pdb=" N ILE A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.593A pdb=" N ARG A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.537A pdb=" N LEU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.736A pdb=" N VAL A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 454 removed outlier: 4.484A pdb=" N VAL A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 4.311A pdb=" N CYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 removed outlier: 4.030A pdb=" N VAL A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 4.224A pdb=" N LEU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 235 removed outlier: 3.966A pdb=" N GLN B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.865A pdb=" N LYS B 245 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.554A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.999A pdb=" N VAL B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 removed outlier: 3.517A pdb=" N LEU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.842A pdb=" N ILE B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 460 removed outlier: 3.649A pdb=" N LEU B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 removed outlier: 4.355A pdb=" N GLU B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.694A pdb=" N ASP B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'C' and resid 28 through 32 No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.963A pdb=" N UNK C 64 " --> pdb=" O UNK C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.974A pdb=" N THR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.535A pdb=" N SER D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.616A pdb=" N GLU D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.684A pdb=" N PHE B 466 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.778A pdb=" N GLN B 279 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 307 removed outlier: 6.648A pdb=" N LEU B 306 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 345 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY B 379 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 399 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.584A pdb=" N HIS B 556 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 542 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY B 621 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER B 598 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 623 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.639A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 21 removed outlier: 3.586A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 129 removed outlier: 6.160A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 129 removed outlier: 6.160A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 174 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.545A pdb=" N THR C 158 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 200 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 4 through 6 current: chain 'D' and resid 20 through 25 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.959A pdb=" N LEU D 11 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.560A pdb=" N ASN D 143 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA D 136 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 138 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR D 179 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 182 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 168 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.873A pdb=" N TRP D 154 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 198 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 215 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 978 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: 3.22 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3051 1.34 - 1.46: 1941 1.46 - 1.57: 5149 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10190 Sorted by residual: bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C SER D 7 " pdb=" N PRO D 8 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.76e+01 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.333 1.369 -0.035 1.01e-02 9.80e+03 1.22e+01 bond pdb=" C ARG A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" C1 NAG B 706 " pdb=" O5 NAG B 706 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 10185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13403 2.21 - 4.41: 438 4.41 - 6.62: 52 6.62 - 8.83: 18 8.83 - 11.03: 7 Bond angle restraints: 13918 Sorted by residual: angle pdb=" C UNK D 56 " pdb=" N UNK D 57 " pdb=" CA UNK D 57 " ideal model delta sigma weight residual 121.70 131.80 -10.10 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N THR A 71 " pdb=" CA THR A 71 " pdb=" C THR A 71 " ideal model delta sigma weight residual 109.81 120.57 -10.76 2.21e+00 2.05e-01 2.37e+01 angle pdb=" C ILE D 156 " pdb=" N ASP D 157 " pdb=" CA ASP D 157 " ideal model delta sigma weight residual 122.46 128.46 -6.00 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C SER A 126 " pdb=" N LEU A 127 " pdb=" CA LEU A 127 " ideal model delta sigma weight residual 120.06 125.12 -5.06 1.19e+00 7.06e-01 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" C LEU B 261 " ideal model delta sigma weight residual 110.35 116.09 -5.74 1.40e+00 5.10e-01 1.68e+01 ... (remaining 13913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 5866 21.25 - 42.51: 391 42.51 - 63.76: 50 63.76 - 85.01: 12 85.01 - 106.27: 3 Dihedral angle restraints: 6322 sinusoidal: 2614 harmonic: 3708 Sorted by residual: dihedral pdb=" CA ARG A 427 " pdb=" C ARG A 427 " pdb=" N PRO A 428 " pdb=" CA PRO A 428 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA A 118 " pdb=" C ALA A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 259 " pdb=" C LEU B 259 " pdb=" N VAL B 260 " pdb=" CA VAL B 260 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1220 0.051 - 0.102: 324 0.102 - 0.153: 91 0.153 - 0.204: 17 0.204 - 0.255: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 424 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.56e+00 ... (remaining 1653 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 372 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 373 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 469 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 470 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 158 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO A 159 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.043 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2958 2.81 - 3.34: 8290 3.34 - 3.86: 15542 3.86 - 4.38: 17629 4.38 - 4.90: 30945 Nonbonded interactions: 75364 Sorted by model distance: nonbonded pdb=" OG SER B 535 " pdb=" O GLU B 561 " model vdw 2.293 3.040 nonbonded pdb=" O TYR B 250 " pdb=" OG SER B 253 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG A 419 " pdb=" OE2 GLU A 426 " model vdw 2.358 3.120 nonbonded pdb=" O ILE A 139 " pdb=" OG SER A 143 " model vdw 2.361 3.040 nonbonded pdb=" O TRP B 363 " pdb=" OG1 THR B 367 " model vdw 2.372 3.040 ... (remaining 75359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.005 0.100 10204 Z= 0.245 Angle : 0.961 11.034 13956 Z= 0.523 Chirality : 0.052 0.255 1656 Planarity : 0.007 0.084 1711 Dihedral : 14.029 106.266 3905 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 0.29 % Allowed : 7.40 % Favored : 92.32 % 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: -5.03 (0.18), residues: 1197 helix: -4.70 (0.09), residues: 437 sheet: -1.52 (0.39), residues: 159 loop : -2.72 (0.20), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 190 HIS 0.004 0.001 HIS D 204 PHE 0.016 0.002 PHE B 551 TYR 0.019 0.002 TYR B 453 ARG 0.006 0.001 ARG A 419 Details of bonding type rmsd link_TRANS : bond 0.00294 ( 5) link_TRANS : angle 0.99175 ( 15) link_NAG-ASN : bond 0.00524 ( 4) link_NAG-ASN : angle 2.62703 ( 12) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 1.44908 ( 3) hydrogen bonds : bond 0.31609 ( 333) hydrogen bonds : angle 10.55796 ( 978) SS BOND : bond 0.00593 ( 4) SS BOND : angle 1.01364 ( 8) covalent geometry : bond 0.00511 (10190) covalent geometry : angle 0.95836 (13918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 111 SER cc_start: 0.7608 (m) cc_final: 0.7130 (p) REVERT: A 134 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7734 (t60) REVERT: A 259 TYR cc_start: 0.7910 (m-80) cc_final: 0.7371 (m-80) REVERT: A 272 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6789 (ptp-170) REVERT: A 325 TRP cc_start: 0.7324 (t60) cc_final: 0.7116 (t-100) REVERT: A 326 ILE cc_start: 0.8628 (tt) cc_final: 0.8369 (tt) REVERT: A 407 CYS cc_start: 0.7519 (m) cc_final: 0.7249 (m) REVERT: A 424 GLU cc_start: 0.7617 (tp30) cc_final: 0.6839 (tm-30) REVERT: B 325 THR cc_start: 0.9133 (p) cc_final: 0.8921 (t) REVERT: B 370 PHE cc_start: 0.8066 (t80) cc_final: 0.7462 (t80) REVERT: B 528 ASP cc_start: 0.8021 (t0) cc_final: 0.7815 (m-30) REVERT: B 607 SER cc_start: 0.8640 (p) cc_final: 0.8029 (m) REVERT: B 625 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7972 (mtm110) REVERT: C 89 ASP cc_start: 0.8085 (m-30) cc_final: 0.7014 (m-30) REVERT: D 6 GLN cc_start: 0.8495 (tt0) cc_final: 0.8218 (mt0) REVERT: D 42 TYR cc_start: 0.9058 (m-80) cc_final: 0.8823 (m-80) REVERT: D 156 ILE cc_start: 0.6044 (mt) cc_final: 0.5819 (mt) REVERT: D 176 ASP cc_start: 0.8609 (p0) cc_final: 0.7738 (p0) REVERT: D 201 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7460 (mm-30) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.2218 time to fit residues: 65.3683 Evaluate side-chains 143 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 186 ASN A 218 GLN A 293 ASN B 267 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 560 ASN C 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125405 restraints weight = 14686.189| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.64 r_work: 0.3191 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10204 Z= 0.155 Angle : 0.660 9.407 13956 Z= 0.330 Chirality : 0.042 0.209 1656 Planarity : 0.006 0.083 1711 Dihedral : 7.723 89.160 1787 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.83 % Allowed : 12.78 % Favored : 85.40 % 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: -3.66 (0.20), residues: 1197 helix: -3.10 (0.18), residues: 444 sheet: -1.03 (0.36), residues: 180 loop : -2.26 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 405 HIS 0.002 0.001 HIS C 204 PHE 0.016 0.001 PHE B 551 TYR 0.011 0.001 TYR B 225 ARG 0.005 0.001 ARG B 439 Details of bonding type rmsd link_TRANS : bond 0.00188 ( 5) link_TRANS : angle 0.73633 ( 15) link_NAG-ASN : bond 0.00372 ( 4) link_NAG-ASN : angle 1.98391 ( 12) link_BETA1-4 : bond 0.00265 ( 1) link_BETA1-4 : angle 1.15475 ( 3) hydrogen bonds : bond 0.05270 ( 333) hydrogen bonds : angle 5.97171 ( 978) SS BOND : bond 0.00325 ( 4) SS BOND : angle 0.98617 ( 8) covalent geometry : bond 0.00357 (10190) covalent geometry : angle 0.65699 (13918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.123 Fit side-chains REVERT: A 54 ASN cc_start: 0.7228 (t160) cc_final: 0.6524 (m110) REVERT: A 134 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7903 (t60) REVERT: A 155 TYR cc_start: 0.9217 (m-80) cc_final: 0.8948 (m-80) REVERT: A 243 ILE cc_start: 0.7969 (tp) cc_final: 0.7712 (tp) REVERT: A 259 TYR cc_start: 0.8175 (m-80) cc_final: 0.7565 (m-80) REVERT: A 272 ARG cc_start: 0.7112 (ptp-170) cc_final: 0.4727 (mmt180) REVERT: A 325 TRP cc_start: 0.7443 (t60) cc_final: 0.7102 (t-100) REVERT: A 326 ILE cc_start: 0.8741 (tt) cc_final: 0.8492 (tt) REVERT: A 348 ARG cc_start: 0.8207 (ptm-80) cc_final: 0.7802 (ptt90) REVERT: A 349 LEU cc_start: 0.8828 (tp) cc_final: 0.8453 (tt) REVERT: A 424 GLU cc_start: 0.8135 (tp30) cc_final: 0.7042 (tm-30) REVERT: B 190 TRP cc_start: 0.5378 (t-100) cc_final: 0.4088 (t60) REVERT: B 231 GLN cc_start: 0.8526 (tp40) cc_final: 0.8292 (tp-100) REVERT: B 255 LYS cc_start: 0.9142 (mttm) cc_final: 0.8812 (mtmm) REVERT: C 89 ASP cc_start: 0.8119 (m-30) cc_final: 0.7036 (m-30) REVERT: C 214 LYS cc_start: 0.8269 (tttm) cc_final: 0.7575 (tttp) REVERT: D 156 ILE cc_start: 0.5532 (mt) cc_final: 0.5231 (mt) outliers start: 19 outliers final: 15 residues processed: 174 average time/residue: 0.2331 time to fit residues: 56.2317 Evaluate side-chains 157 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 HIS D 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115654 restraints weight = 14706.196| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.43 r_work: 0.3250 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10204 Z= 0.170 Angle : 0.657 8.625 13956 Z= 0.320 Chirality : 0.043 0.232 1656 Planarity : 0.005 0.081 1711 Dihedral : 7.297 87.357 1787 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 14.79 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1197 helix: -2.16 (0.21), residues: 448 sheet: -0.58 (0.38), residues: 178 loop : -2.04 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 190 HIS 0.002 0.001 HIS D 204 PHE 0.016 0.001 PHE A 336 TYR 0.014 0.002 TYR B 225 ARG 0.005 0.001 ARG B 625 Details of bonding type rmsd link_TRANS : bond 0.00272 ( 5) link_TRANS : angle 0.69776 ( 15) link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 1.84969 ( 12) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 1.27992 ( 3) hydrogen bonds : bond 0.04320 ( 333) hydrogen bonds : angle 5.29526 ( 978) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.99132 ( 8) covalent geometry : bond 0.00401 (10190) covalent geometry : angle 0.65337 (13918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.126 Fit side-chains REVERT: A 134 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7849 (t60) REVERT: A 272 ARG cc_start: 0.7070 (ptp-170) cc_final: 0.4436 (mmt180) REVERT: A 325 TRP cc_start: 0.7567 (t60) cc_final: 0.7067 (t-100) REVERT: A 348 ARG cc_start: 0.8207 (ptm-80) cc_final: 0.7799 (ptt90) REVERT: A 349 LEU cc_start: 0.8799 (tp) cc_final: 0.8369 (tt) REVERT: A 424 GLU cc_start: 0.8281 (tp30) cc_final: 0.7204 (tm-30) REVERT: B 190 TRP cc_start: 0.5408 (t-100) cc_final: 0.4371 (t60) REVERT: B 231 GLN cc_start: 0.8647 (tp40) cc_final: 0.8389 (tp-100) REVERT: B 353 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8190 (pt) REVERT: B 372 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: B 528 ASP cc_start: 0.8516 (t0) cc_final: 0.8075 (m-30) REVERT: C 89 ASP cc_start: 0.8172 (m-30) cc_final: 0.7068 (m-30) REVERT: C 214 LYS cc_start: 0.8183 (tttm) cc_final: 0.7851 (tttp) REVERT: D 17 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8156 (mt-10) REVERT: D 129 GLU cc_start: 0.7340 (tt0) cc_final: 0.6708 (mp0) REVERT: D 156 ILE cc_start: 0.5539 (mt) cc_final: 0.5264 (mt) REVERT: D 185 LEU cc_start: 0.7118 (mt) cc_final: 0.6846 (mt) outliers start: 33 outliers final: 23 residues processed: 167 average time/residue: 0.1996 time to fit residues: 48.2600 Evaluate side-chains 166 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 295 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117219 restraints weight = 14523.517| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.46 r_work: 0.3238 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10204 Z= 0.166 Angle : 0.635 7.846 13956 Z= 0.309 Chirality : 0.043 0.227 1656 Planarity : 0.005 0.077 1711 Dihedral : 6.947 83.129 1787 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.46 % Allowed : 15.75 % Favored : 80.79 % 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: -2.44 (0.22), residues: 1197 helix: -1.65 (0.22), residues: 455 sheet: -0.63 (0.37), residues: 190 loop : -1.87 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 190 HIS 0.003 0.001 HIS C 204 PHE 0.014 0.001 PHE A 336 TYR 0.013 0.001 TYR B 225 ARG 0.004 0.001 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00243 ( 5) link_TRANS : angle 0.63082 ( 15) link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 1.82071 ( 12) link_BETA1-4 : bond 0.00231 ( 1) link_BETA1-4 : angle 1.32947 ( 3) hydrogen bonds : bond 0.03790 ( 333) hydrogen bonds : angle 4.96971 ( 978) SS BOND : bond 0.00370 ( 4) SS BOND : angle 2.11846 ( 8) covalent geometry : bond 0.00397 (10190) covalent geometry : angle 0.63063 (13918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.062 Fit side-chains REVERT: A 134 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7828 (t60) REVERT: A 259 TYR cc_start: 0.7816 (m-80) cc_final: 0.7365 (m-80) REVERT: A 272 ARG cc_start: 0.7108 (ptp-170) cc_final: 0.4807 (mmt180) REVERT: A 325 TRP cc_start: 0.7567 (t60) cc_final: 0.7149 (t-100) REVERT: A 348 ARG cc_start: 0.8332 (ptm-80) cc_final: 0.7977 (ptt90) REVERT: A 349 LEU cc_start: 0.8801 (tp) cc_final: 0.8332 (tt) REVERT: A 424 GLU cc_start: 0.8241 (tp30) cc_final: 0.7313 (tm-30) REVERT: B 190 TRP cc_start: 0.5185 (t-100) cc_final: 0.4351 (t60) REVERT: B 353 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8261 (pt) REVERT: B 528 ASP cc_start: 0.8506 (t0) cc_final: 0.8201 (m-30) REVERT: C 81 LYS cc_start: 0.8743 (tppt) cc_final: 0.8480 (mmtt) REVERT: C 89 ASP cc_start: 0.8225 (m-30) cc_final: 0.7032 (m-30) REVERT: C 214 LYS cc_start: 0.8241 (tttm) cc_final: 0.7869 (tttp) REVERT: D 129 GLU cc_start: 0.7448 (tt0) cc_final: 0.6817 (mp0) REVERT: D 151 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: D 156 ILE cc_start: 0.5375 (mt) cc_final: 0.5129 (mt) REVERT: D 185 LEU cc_start: 0.7366 (mt) cc_final: 0.7029 (mt) outliers start: 36 outliers final: 26 residues processed: 170 average time/residue: 0.2181 time to fit residues: 52.4407 Evaluate side-chains 167 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118616 restraints weight = 14625.092| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.36 r_work: 0.3274 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10204 Z= 0.130 Angle : 0.604 8.539 13956 Z= 0.292 Chirality : 0.041 0.215 1656 Planarity : 0.005 0.077 1711 Dihedral : 6.597 78.264 1787 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.46 % Allowed : 16.62 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.22), residues: 1197 helix: -1.19 (0.23), residues: 457 sheet: -0.51 (0.38), residues: 183 loop : -1.77 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 190 HIS 0.003 0.001 HIS C 204 PHE 0.017 0.001 PHE A 402 TYR 0.010 0.001 TYR B 225 ARG 0.004 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00170 ( 5) link_TRANS : angle 0.49547 ( 15) link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.75071 ( 12) link_BETA1-4 : bond 0.00220 ( 1) link_BETA1-4 : angle 1.23871 ( 3) hydrogen bonds : bond 0.03411 ( 333) hydrogen bonds : angle 4.76949 ( 978) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.97823 ( 8) covalent geometry : bond 0.00306 (10190) covalent geometry : angle 0.60058 (13918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.028 Fit side-chains REVERT: A 134 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7757 (t60) REVERT: A 259 TYR cc_start: 0.7901 (m-80) cc_final: 0.7526 (m-80) REVERT: A 272 ARG cc_start: 0.6965 (ptp-170) cc_final: 0.4601 (mmt180) REVERT: A 317 ASN cc_start: 0.8049 (m-40) cc_final: 0.7721 (m-40) REVERT: A 325 TRP cc_start: 0.7540 (t60) cc_final: 0.7088 (t-100) REVERT: A 348 ARG cc_start: 0.8331 (ptm-80) cc_final: 0.7970 (ptt90) REVERT: A 349 LEU cc_start: 0.8756 (tp) cc_final: 0.8290 (tt) REVERT: A 424 GLU cc_start: 0.8235 (tp30) cc_final: 0.7439 (tm-30) REVERT: B 190 TRP cc_start: 0.5294 (t-100) cc_final: 0.4689 (t60) REVERT: B 308 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8389 (mm) REVERT: B 353 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8225 (pt) REVERT: B 440 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8599 (mp) REVERT: B 528 ASP cc_start: 0.8336 (t0) cc_final: 0.8020 (m-30) REVERT: C 81 LYS cc_start: 0.8805 (tppt) cc_final: 0.8534 (mmtt) REVERT: C 89 ASP cc_start: 0.8083 (m-30) cc_final: 0.6964 (m-30) REVERT: C 140 MET cc_start: 0.6465 (mmt) cc_final: 0.6169 (mmp) REVERT: C 176 GLN cc_start: 0.8215 (tt0) cc_final: 0.7112 (pp30) REVERT: C 214 LYS cc_start: 0.8178 (tttm) cc_final: 0.7663 (tttp) REVERT: D 17 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8015 (mt-10) REVERT: D 129 GLU cc_start: 0.7583 (tt0) cc_final: 0.6934 (mp0) REVERT: D 151 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: D 185 LEU cc_start: 0.7610 (mt) cc_final: 0.7265 (mt) outliers start: 36 outliers final: 29 residues processed: 175 average time/residue: 0.2243 time to fit residues: 55.6806 Evaluate side-chains 172 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117700 restraints weight = 14585.326| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.50 r_work: 0.3257 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10204 Z= 0.128 Angle : 0.602 9.748 13956 Z= 0.288 Chirality : 0.041 0.208 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.322 74.173 1787 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.32 % Allowed : 16.04 % Favored : 79.63 % 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: -1.74 (0.23), residues: 1197 helix: -0.85 (0.23), residues: 459 sheet: -0.19 (0.39), residues: 173 loop : -1.68 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 204 PHE 0.014 0.001 PHE A 336 TYR 0.015 0.001 TYR A 318 ARG 0.005 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00176 ( 5) link_TRANS : angle 0.50277 ( 15) link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 1.84832 ( 12) link_BETA1-4 : bond 0.00282 ( 1) link_BETA1-4 : angle 1.23337 ( 3) hydrogen bonds : bond 0.03308 ( 333) hydrogen bonds : angle 4.64722 ( 978) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.80561 ( 8) covalent geometry : bond 0.00305 (10190) covalent geometry : angle 0.59873 (13918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7692 (t60) REVERT: A 259 TYR cc_start: 0.8017 (m-80) cc_final: 0.7570 (m-80) REVERT: A 272 ARG cc_start: 0.6898 (ptp-170) cc_final: 0.4570 (mmt180) REVERT: A 325 TRP cc_start: 0.7507 (t60) cc_final: 0.6948 (t-100) REVERT: A 348 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.7974 (ptt90) REVERT: A 349 LEU cc_start: 0.8736 (tp) cc_final: 0.8293 (tt) REVERT: A 386 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 424 GLU cc_start: 0.8284 (tp30) cc_final: 0.7523 (tm-30) REVERT: B 190 TRP cc_start: 0.5383 (t-100) cc_final: 0.4881 (t60) REVERT: B 274 GLN cc_start: 0.8474 (mt0) cc_final: 0.8108 (mt0) REVERT: B 308 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8423 (mm) REVERT: B 353 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8263 (pt) REVERT: B 528 ASP cc_start: 0.8504 (t0) cc_final: 0.8297 (m-30) REVERT: C 81 LYS cc_start: 0.8749 (tppt) cc_final: 0.8440 (mmtt) REVERT: C 89 ASP cc_start: 0.8076 (m-30) cc_final: 0.6942 (m-30) REVERT: C 176 GLN cc_start: 0.8221 (tt0) cc_final: 0.7074 (pp30) REVERT: C 201 ASN cc_start: 0.7260 (p0) cc_final: 0.6713 (p0) REVERT: C 214 LYS cc_start: 0.8076 (tttm) cc_final: 0.7558 (tttp) REVERT: D 17 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 129 GLU cc_start: 0.7479 (tt0) cc_final: 0.6827 (mp0) REVERT: D 151 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8317 (m-40) REVERT: D 185 LEU cc_start: 0.7668 (mt) cc_final: 0.7277 (mt) outliers start: 45 outliers final: 32 residues processed: 179 average time/residue: 0.2094 time to fit residues: 53.8858 Evaluate side-chains 176 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118968 restraints weight = 14769.017| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.42 r_work: 0.3265 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10204 Z= 0.131 Angle : 0.606 8.345 13956 Z= 0.291 Chirality : 0.041 0.198 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.128 69.965 1787 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.03 % Allowed : 16.43 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1197 helix: -0.64 (0.24), residues: 458 sheet: -0.34 (0.38), residues: 183 loop : -1.62 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.016 0.001 TYR A 318 ARG 0.005 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00183 ( 5) link_TRANS : angle 0.51274 ( 15) link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 1.91298 ( 12) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 1.19064 ( 3) hydrogen bonds : bond 0.03265 ( 333) hydrogen bonds : angle 4.60856 ( 978) SS BOND : bond 0.00379 ( 4) SS BOND : angle 1.81164 ( 8) covalent geometry : bond 0.00313 (10190) covalent geometry : angle 0.60263 (13918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7707 (t60) REVERT: A 259 TYR cc_start: 0.8013 (m-80) cc_final: 0.7558 (m-80) REVERT: A 272 ARG cc_start: 0.6925 (ptp-170) cc_final: 0.4585 (mmt180) REVERT: A 325 TRP cc_start: 0.7550 (t60) cc_final: 0.6965 (t-100) REVERT: A 348 ARG cc_start: 0.8323 (ptm-80) cc_final: 0.7964 (ptt90) REVERT: A 349 LEU cc_start: 0.8773 (tp) cc_final: 0.8368 (tt) REVERT: A 386 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 424 GLU cc_start: 0.8267 (tp30) cc_final: 0.7545 (tm-30) REVERT: B 190 TRP cc_start: 0.5500 (t-100) cc_final: 0.4970 (t60) REVERT: B 274 GLN cc_start: 0.8383 (mt0) cc_final: 0.8078 (mt0) REVERT: B 308 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 353 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8272 (pt) REVERT: C 89 ASP cc_start: 0.8103 (m-30) cc_final: 0.6991 (m-30) REVERT: C 176 GLN cc_start: 0.8257 (tt0) cc_final: 0.7136 (pp30) REVERT: C 201 ASN cc_start: 0.7202 (p0) cc_final: 0.6712 (p0) REVERT: C 214 LYS cc_start: 0.8046 (tttm) cc_final: 0.7534 (tttp) REVERT: D 17 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 129 GLU cc_start: 0.7472 (tt0) cc_final: 0.6841 (mp0) REVERT: D 151 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: D 185 LEU cc_start: 0.7694 (mt) cc_final: 0.7293 (mt) outliers start: 42 outliers final: 34 residues processed: 174 average time/residue: 0.1992 time to fit residues: 49.5419 Evaluate side-chains 176 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117658 restraints weight = 14849.615| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.40 r_work: 0.3236 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10204 Z= 0.172 Angle : 0.643 7.765 13956 Z= 0.310 Chirality : 0.043 0.197 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.171 67.276 1787 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.61 % Allowed : 16.23 % Favored : 79.15 % 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: -1.61 (0.23), residues: 1197 helix: -0.62 (0.24), residues: 458 sheet: -0.37 (0.37), residues: 190 loop : -1.65 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS A 420 PHE 0.013 0.001 PHE C 151 TYR 0.015 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00235 ( 5) link_TRANS : angle 0.64445 ( 15) link_NAG-ASN : bond 0.00136 ( 4) link_NAG-ASN : angle 2.05064 ( 12) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.23333 ( 3) hydrogen bonds : bond 0.03469 ( 333) hydrogen bonds : angle 4.68672 ( 978) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.82336 ( 8) covalent geometry : bond 0.00415 (10190) covalent geometry : angle 0.63914 (13918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.009 Fit side-chains REVERT: A 134 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7743 (t60) REVERT: A 259 TYR cc_start: 0.8113 (m-80) cc_final: 0.7687 (m-80) REVERT: A 272 ARG cc_start: 0.6965 (ptp-170) cc_final: 0.4617 (mmt180) REVERT: A 318 TYR cc_start: 0.7483 (t80) cc_final: 0.7273 (t80) REVERT: A 325 TRP cc_start: 0.7574 (t60) cc_final: 0.6940 (t-100) REVERT: A 348 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.8020 (ptt90) REVERT: A 349 LEU cc_start: 0.8810 (tp) cc_final: 0.8378 (tt) REVERT: A 386 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 424 GLU cc_start: 0.8262 (tp30) cc_final: 0.7561 (tm-30) REVERT: B 190 TRP cc_start: 0.5599 (t-100) cc_final: 0.5086 (t60) REVERT: B 274 GLN cc_start: 0.8372 (mt0) cc_final: 0.8071 (mt0) REVERT: B 308 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 353 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8319 (pt) REVERT: C 89 ASP cc_start: 0.8101 (m-30) cc_final: 0.6601 (m-30) REVERT: C 176 GLN cc_start: 0.8239 (tt0) cc_final: 0.7077 (pp30) REVERT: C 201 ASN cc_start: 0.7347 (p0) cc_final: 0.6934 (p0) REVERT: C 214 LYS cc_start: 0.8051 (tttm) cc_final: 0.7619 (tttp) REVERT: D 17 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8064 (mt-10) REVERT: D 129 GLU cc_start: 0.7487 (tt0) cc_final: 0.6861 (mp0) REVERT: D 151 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: D 185 LEU cc_start: 0.7693 (mt) cc_final: 0.7279 (mt) outliers start: 48 outliers final: 36 residues processed: 175 average time/residue: 0.2089 time to fit residues: 52.2797 Evaluate side-chains 177 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 91 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118369 restraints weight = 14716.294| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.31 r_work: 0.3287 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10204 Z= 0.113 Angle : 0.596 8.820 13956 Z= 0.285 Chirality : 0.040 0.160 1656 Planarity : 0.005 0.075 1711 Dihedral : 5.767 59.084 1787 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.75 % Allowed : 17.58 % Favored : 78.67 % 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: -1.37 (0.23), residues: 1197 helix: -0.36 (0.24), residues: 459 sheet: -0.26 (0.38), residues: 183 loop : -1.57 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 190 HIS 0.002 0.000 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.016 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00136 ( 5) link_TRANS : angle 0.41050 ( 15) link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 2.03951 ( 12) link_BETA1-4 : bond 0.00228 ( 1) link_BETA1-4 : angle 1.06584 ( 3) hydrogen bonds : bond 0.03089 ( 333) hydrogen bonds : angle 4.54869 ( 978) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.71738 ( 8) covalent geometry : bond 0.00266 (10190) covalent geometry : angle 0.59165 (13918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7744 (t60) REVERT: A 259 TYR cc_start: 0.8121 (m-80) cc_final: 0.7714 (m-80) REVERT: A 272 ARG cc_start: 0.7007 (ptp-170) cc_final: 0.4604 (mmt180) REVERT: A 325 TRP cc_start: 0.7557 (t60) cc_final: 0.6911 (t-100) REVERT: A 348 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.8093 (ptt90) REVERT: A 349 LEU cc_start: 0.8765 (tp) cc_final: 0.8392 (tt) REVERT: A 386 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 424 GLU cc_start: 0.8238 (tp30) cc_final: 0.7620 (tm-30) REVERT: B 187 LEU cc_start: 0.7244 (tp) cc_final: 0.7028 (tp) REVERT: B 190 TRP cc_start: 0.5618 (t-100) cc_final: 0.4947 (t60) REVERT: B 274 GLN cc_start: 0.8166 (mt0) cc_final: 0.7922 (mt0) REVERT: B 308 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 353 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8247 (pt) REVERT: B 528 ASP cc_start: 0.8139 (t0) cc_final: 0.7876 (m-30) REVERT: B 588 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8724 (m) REVERT: C 89 ASP cc_start: 0.7940 (m-30) cc_final: 0.6930 (m-30) REVERT: C 176 GLN cc_start: 0.8314 (tt0) cc_final: 0.7225 (pp30) REVERT: C 201 ASN cc_start: 0.7283 (p0) cc_final: 0.6875 (p0) REVERT: C 214 LYS cc_start: 0.7935 (tttm) cc_final: 0.7467 (tttp) REVERT: D 17 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 129 GLU cc_start: 0.7485 (tt0) cc_final: 0.6887 (mp0) REVERT: D 151 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: D 185 LEU cc_start: 0.7700 (mt) cc_final: 0.7304 (mt) outliers start: 39 outliers final: 28 residues processed: 172 average time/residue: 0.2204 time to fit residues: 55.3477 Evaluate side-chains 174 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117355 restraints weight = 14740.860| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.31 r_work: 0.3273 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10204 Z= 0.130 Angle : 0.624 9.521 13956 Z= 0.295 Chirality : 0.041 0.155 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.657 55.652 1787 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 3.36 % Allowed : 17.68 % Favored : 78.96 % 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: -1.29 (0.23), residues: 1197 helix: -0.23 (0.24), residues: 461 sheet: -0.26 (0.39), residues: 183 loop : -1.57 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 169 HIS 0.003 0.001 HIS A 319 PHE 0.014 0.001 PHE A 336 TYR 0.014 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00168 ( 5) link_TRANS : angle 0.51456 ( 15) link_NAG-ASN : bond 0.00171 ( 4) link_NAG-ASN : angle 2.12473 ( 12) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 1.12109 ( 3) hydrogen bonds : bond 0.03132 ( 333) hydrogen bonds : angle 4.51698 ( 978) SS BOND : bond 0.00342 ( 4) SS BOND : angle 1.75384 ( 8) covalent geometry : bond 0.00313 (10190) covalent geometry : angle 0.61956 (13918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7789 (t60) REVERT: A 259 TYR cc_start: 0.8198 (m-80) cc_final: 0.7819 (m-80) REVERT: A 272 ARG cc_start: 0.7126 (ptp-170) cc_final: 0.4884 (mmt180) REVERT: A 325 TRP cc_start: 0.7502 (t60) cc_final: 0.6811 (t-100) REVERT: A 348 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.8001 (ptt90) REVERT: A 349 LEU cc_start: 0.8781 (tp) cc_final: 0.8409 (tt) REVERT: A 386 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 405 TRP cc_start: 0.8626 (m100) cc_final: 0.8381 (m100) REVERT: A 424 GLU cc_start: 0.8302 (tp30) cc_final: 0.7691 (tm-30) REVERT: B 190 TRP cc_start: 0.5879 (t-100) cc_final: 0.5179 (t60) REVERT: B 274 GLN cc_start: 0.8186 (mt0) cc_final: 0.7938 (mt0) REVERT: B 353 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8279 (pt) REVERT: B 588 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8768 (m) REVERT: C 89 ASP cc_start: 0.8035 (m-30) cc_final: 0.6925 (m-30) REVERT: C 176 GLN cc_start: 0.8320 (tt0) cc_final: 0.7219 (pp30) REVERT: C 201 ASN cc_start: 0.7391 (p0) cc_final: 0.7013 (p0) REVERT: C 214 LYS cc_start: 0.7916 (tttm) cc_final: 0.7447 (tttp) REVERT: D 17 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7958 (mt-10) REVERT: D 129 GLU cc_start: 0.7481 (tt0) cc_final: 0.6880 (mp0) REVERT: D 151 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8239 (m-40) REVERT: D 185 LEU cc_start: 0.7737 (mt) cc_final: 0.7335 (mt) outliers start: 35 outliers final: 27 residues processed: 166 average time/residue: 0.2297 time to fit residues: 55.8896 Evaluate side-chains 166 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117096 restraints weight = 14674.314| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.30 r_work: 0.3275 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10204 Z= 0.140 Angle : 0.654 9.795 13956 Z= 0.311 Chirality : 0.041 0.152 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.806 54.617 1787 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 17.87 % Favored : 78.77 % Cbeta Deviations : 0.08 % 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: -1.23 (0.24), residues: 1197 helix: -0.16 (0.24), residues: 460 sheet: -0.29 (0.39), residues: 182 loop : -1.53 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.015 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 Details of bonding type rmsd link_TRANS : bond 0.00183 ( 5) link_TRANS : angle 0.54011 ( 15) link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 2.15492 ( 12) link_BETA1-4 : bond 0.00256 ( 1) link_BETA1-4 : angle 1.11705 ( 3) hydrogen bonds : bond 0.03124 ( 333) hydrogen bonds : angle 4.52119 ( 978) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.73295 ( 8) covalent geometry : bond 0.00338 (10190) covalent geometry : angle 0.65020 (13918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6465.84 seconds wall clock time: 112 minutes 19.92 seconds (6739.92 seconds total)