Starting phenix.real_space_refine on Fri Sep 11 16:03:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jmq_9849/09_2026/6jmq_9849.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 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 chiralities: 3 Time building chain proxies: 2.08, per 1000 atoms: 0.21 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: 0.93 Conformation dependent library (CDL) restraints added in 253.5 milliseconds 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: 0.22 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: 1.49 Time building geometry restraints manager: 1.13 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 - 16.93: 5321 16.93 - 33.87: 493 33.87 - 50.80: 100 50.80 - 67.73: 15 67.73 - 84.67: 8 Dihedral angle restraints: 5937 sinusoidal: 2229 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 5934 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 13.846 84.668 3520 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG A 419 TYR 0.019 0.002 TYR B 453 PHE 0.016 0.002 PHE B 551 TRP 0.017 0.002 TRP B 190 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (10190) covalent geometry : angle 0.95836 / 0.52 (13918) SS BOND : bond 0.00593 / 0.29 ( 4) SS BOND : angle 1.01364 / 0.57 ( 8) hydrogen bonds : bond 0.31609 / 21.07 ( 333) hydrogen bonds : angle 10.55796 / 7.25 ( 978) link_BETA1-4 : bond 0.00383 / 0.20 ( 1) link_BETA1-4 : angle 1.44908 / 0.67 ( 3) link_NAG-ASN : bond 0.00524 / 0.25 ( 4) link_NAG-ASN : angle 2.62703 / 1.33 ( 12) link_TRANS : bond 0.00294 / 0.13 ( 5) link_TRANS : angle 0.99175 / 0.56 ( 15) *********************** 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 : 0.508 Fit side-chains revert: symmetry clash REVERT: A 111 SER cc_start: 0.7608 (m) cc_final: 0.7131 (p) REVERT: A 134 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7735 (t60) REVERT: A 259 TYR cc_start: 0.7910 (m-80) cc_final: 0.7369 (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: 0.8367 (tt) REVERT: A 407 CYS cc_start: 0.7519 (m) cc_final: 0.7247 (m) REVERT: A 424 GLU cc_start: 0.7617 (tp30) cc_final: 0.6840 (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: 0.7461 (t80) REVERT: B 528 ASP cc_start: 0.8021 (t0) cc_final: 0.7816 (m-30) REVERT: B 607 SER cc_start: 0.8640 (p) cc_final: 0.8032 (m) REVERT: B 625 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7969 (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: 0.8217 (mt0) REVERT: D 42 TYR cc_start: 0.9058 (m-80) cc_final: 0.8822 (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: 0.7739 (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: 0.0868 time to fit residues: 25.7176 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 : 0.358 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.159129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119419 restraints weight = 14739.377| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.54 r_work: 0.3275 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1625 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= 0.147 Angle : 0.658 8.520 13956 Z= 0.331 Chirality : 0.042 0.324 1656 Planarity : 0.006 0.083 1711 Dihedral : 5.560 39.564 1402 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.63 % Allowed : 13.16 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.20), residues: 1197 helix: -3.11 (0.18), residues: 447 sheet: -1.00 (0.36), residues: 179 loop : -2.31 (0.21), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 439 TYR 0.011 0.001 TYR B 453 PHE 0.016 0.001 PHE A 336 TRP 0.012 0.001 TRP A 405 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10190) covalent geometry : angle 0.65537 / 0.33 (13918) SS BOND : bond 0.00343 / 0.17 ( 4) SS BOND : angle 0.99402 / 0.53 ( 8) hydrogen bonds : bond 0.05703 / 3.73 ( 333) hydrogen bonds : angle 6.13502 / 4.21 ( 978) link_BETA1-4 : bond 0.00104 / 0.05 ( 1) link_BETA1-4 : angle 0.95753 / 0.39 ( 3) link_NAG-ASN : bond 0.00466 / 0.21 ( 4) link_NAG-ASN : angle 2.00584 / 0.93 ( 12) link_TRANS : bond 0.00219 / 0.10 ( 5) link_TRANS : angle 0.70393 / 0.39 ( 15) *********************** 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 179 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.410 Fit side-chains REVERT: A 54 ASN cc_start: 0.7267 (t0) cc_final: 0.6422 (m110) REVERT: A 111 SER cc_start: 0.7799 (m) cc_final: 0.7329 (p) REVERT: A 134 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7891 (t60) REVERT: A 136 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8148 (mt-10) REVERT: A 155 TYR cc_start: 0.9141 (m-80) cc_final: 0.8926 (m-80) REVERT: A 243 ILE cc_start: 0.7932 (tp) cc_final: 0.7673 (tp) REVERT: A 272 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.4738 (mmt180) REVERT: A 325 TRP cc_start: 0.7406 (t60) cc_final: 0.7110 (t-100) REVERT: A 326 ILE cc_start: 0.8715 (tt) cc_final: 0.8463 (tt) REVERT: A 348 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7813 (ptt90) REVERT: A 349 LEU cc_start: 0.8880 (tp) cc_final: 0.8481 (tt) REVERT: A 424 GLU cc_start: 0.7972 (tp30) cc_final: 0.6902 (tm-30) REVERT: B 190 TRP cc_start: 0.5215 (t-100) cc_final: 0.3915 (t60) REVERT: B 231 GLN cc_start: 0.8445 (tp40) cc_final: 0.8188 (tp-100) REVERT: B 255 LYS cc_start: 0.9092 (mttm) cc_final: 0.8759 (mtmm) REVERT: C 89 ASP cc_start: 0.8118 (m-30) cc_final: 0.7052 (m-30) REVERT: C 212 ASP cc_start: 0.8095 (m-30) cc_final: 0.7893 (m-30) REVERT: C 214 LYS cc_start: 0.8294 (tttm) cc_final: 0.7630 (tttp) REVERT: D 156 ILE cc_start: 0.5560 (mt) cc_final: 0.5311 (mt) REVERT: D 185 LEU cc_start: 0.7304 (tp) cc_final: 0.6997 (mt) REVERT: D 198 TYR cc_start: 0.6936 (m-80) cc_final: 0.6673 (m-80) outliers start: 17 outliers final: 12 residues processed: 173 average time/residue: 0.0916 time to fit residues: 22.6067 Evaluate side-chains 155 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3907 r_free = 0.3907 target = 0.159373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120826 restraints weight = 14702.576| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.43 r_work: 0.3266 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10204 Z= 0.134 Angle : 0.618 8.553 13956 Z= 0.301 Chirality : 0.042 0.335 1656 Planarity : 0.005 0.081 1711 Dihedral : 5.189 42.037 1402 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.40 % Allowed : 14.79 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.21), residues: 1197 helix: -2.16 (0.21), residues: 452 sheet: -0.55 (0.38), residues: 175 loop : -2.02 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 613 TYR 0.013 0.001 TYR A 318 PHE 0.017 0.001 PHE A 336 TRP 0.009 0.001 TRP B 219 HIS 0.002 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10190) covalent geometry : angle 0.61495 / 0.30 (13918) SS BOND : bond 0.00256 / 0.12 ( 4) SS BOND : angle 1.87471 / 0.97 ( 8) hydrogen bonds : bond 0.04024 / 2.65 ( 333) hydrogen bonds : angle 5.24354 / 3.65 ( 978) link_BETA1-4 : bond 0.00191 / 0.10 ( 1) link_BETA1-4 : angle 0.98602 / 0.45 ( 3) link_NAG-ASN : bond 0.00435 / 0.20 ( 4) link_NAG-ASN : angle 1.65567 / 0.75 ( 12) link_TRANS : bond 0.00214 / 0.10 ( 5) link_TRANS : angle 0.53583 / 0.30 ( 15) *********************** 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 175 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.384 Fit side-chains REVERT: A 134 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7859 (t60) REVERT: A 155 TYR cc_start: 0.9196 (m-80) cc_final: 0.8891 (m-80) REVERT: A 259 TYR cc_start: 0.7765 (m-80) cc_final: 0.7284 (m-80) REVERT: A 272 ARG cc_start: 0.7065 (ptp-170) cc_final: 0.4438 (mmt180) REVERT: A 325 TRP cc_start: 0.7512 (t60) cc_final: 0.7101 (t-100) REVERT: A 326 ILE cc_start: 0.8725 (tt) cc_final: 0.8455 (tt) REVERT: A 348 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.7941 (ptt90) REVERT: A 349 LEU cc_start: 0.8776 (tp) cc_final: 0.8339 (tt) REVERT: A 424 GLU cc_start: 0.8224 (tp30) cc_final: 0.7127 (tm-30) REVERT: B 190 TRP cc_start: 0.5245 (t-100) cc_final: 0.4326 (t60) REVERT: B 231 GLN cc_start: 0.8779 (tp40) cc_final: 0.8543 (tp-100) REVERT: B 353 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8081 (pt) REVERT: B 528 ASP cc_start: 0.8494 (t0) cc_final: 0.8203 (m-30) REVERT: C 81 LYS cc_start: 0.8682 (tppt) cc_final: 0.8276 (tppt) REVERT: C 89 ASP cc_start: 0.8042 (m-30) cc_final: 0.6885 (m-30) REVERT: C 214 LYS cc_start: 0.8178 (tttm) cc_final: 0.7797 (tttp) REVERT: D 17 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8154 (mt-10) REVERT: D 156 ILE cc_start: 0.5739 (mt) cc_final: 0.5426 (mt) outliers start: 25 outliers final: 16 residues processed: 167 average time/residue: 0.0944 time to fit residues: 22.2690 Evaluate side-chains 155 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 267 ASN 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 C residue 21 THR 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 D residue 151 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.0020 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 HIS ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119204 restraints weight = 14658.571| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.57 r_work: 0.3265 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10204 Z= 0.113 Angle : 0.584 7.731 13956 Z= 0.284 Chirality : 0.041 0.322 1656 Planarity : 0.005 0.078 1711 Dihedral : 4.931 43.643 1402 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.88 % Allowed : 15.56 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.22), residues: 1197 helix: -1.58 (0.22), residues: 455 sheet: -0.23 (0.39), residues: 173 loop : -1.86 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 613 TYR 0.009 0.001 TYR B 453 PHE 0.016 0.001 PHE A 336 TRP 0.009 0.001 TRP B 219 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10190) covalent geometry : angle 0.58121 / 0.28 (13918) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 1.82897 / 0.95 ( 8) hydrogen bonds : bond 0.03532 / 2.30 ( 333) hydrogen bonds : angle 4.90012 / 3.43 ( 978) link_BETA1-4 : bond 0.00412 / 0.22 ( 1) link_BETA1-4 : angle 1.05758 / 0.50 ( 3) link_NAG-ASN : bond 0.00395 / 0.17 ( 4) link_NAG-ASN : angle 1.47034 / 0.67 ( 12) link_TRANS : bond 0.00146 / 0.06 ( 5) link_TRANS : angle 0.44467 / 0.25 ( 15) *********************** 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 178 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7734 (t60) REVERT: A 259 TYR cc_start: 0.7805 (m-80) cc_final: 0.7240 (m-80) REVERT: A 272 ARG cc_start: 0.6996 (ptp-170) cc_final: 0.4516 (mmt180) REVERT: A 325 TRP cc_start: 0.7529 (t60) cc_final: 0.7099 (t-100) REVERT: A 348 ARG cc_start: 0.8233 (ptm-80) cc_final: 0.7894 (ptt90) REVERT: A 349 LEU cc_start: 0.8731 (tp) cc_final: 0.8298 (tt) REVERT: A 424 GLU cc_start: 0.8113 (tp30) cc_final: 0.7231 (tm-30) REVERT: A 458 CYS cc_start: 0.7519 (m) cc_final: 0.7304 (m) REVERT: B 190 TRP cc_start: 0.4870 (t-100) cc_final: 0.4280 (t60) REVERT: B 353 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7993 (pt) REVERT: B 596 LEU cc_start: 0.9170 (tp) cc_final: 0.8916 (tt) REVERT: C 81 LYS cc_start: 0.8701 (tppt) cc_final: 0.8386 (mmtt) REVERT: C 89 ASP cc_start: 0.7949 (m-30) cc_final: 0.6939 (m-30) REVERT: C 214 LYS cc_start: 0.8102 (tttm) cc_final: 0.7789 (tttp) REVERT: D 17 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7814 (mt-10) REVERT: D 151 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8182 (m-40) REVERT: D 156 ILE cc_start: 0.5532 (mt) cc_final: 0.5283 (mt) outliers start: 30 outliers final: 22 residues processed: 169 average time/residue: 0.0917 time to fit residues: 21.9559 Evaluate side-chains 160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 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 C residue 21 THR Chi-restraints excluded: chain C residue 23 THR 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 76 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119527 restraints weight = 14675.867| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.43 r_work: 0.3260 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10204 Z= 0.144 Angle : 0.603 7.309 13956 Z= 0.295 Chirality : 0.042 0.322 1656 Planarity : 0.005 0.077 1711 Dihedral : 4.914 44.339 1402 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.36 % Allowed : 15.56 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.23), residues: 1197 helix: -1.16 (0.23), residues: 458 sheet: -0.44 (0.37), residues: 190 loop : -1.78 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 613 TYR 0.012 0.001 TYR A 318 PHE 0.014 0.001 PHE A 336 TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (10190) covalent geometry : angle 0.59997 / 0.29 (13918) SS BOND : bond 0.00365 / 0.17 ( 4) SS BOND : angle 1.75684 / 0.92 ( 8) hydrogen bonds : bond 0.03517 / 2.31 ( 333) hydrogen bonds : angle 4.75347 / 3.32 ( 978) link_BETA1-4 : bond 0.00109 / 0.06 ( 1) link_BETA1-4 : angle 1.02421 / 0.47 ( 3) link_NAG-ASN : bond 0.00337 / 0.14 ( 4) link_NAG-ASN : angle 1.57997 / 0.70 ( 12) link_TRANS : bond 0.00206 / 0.09 ( 5) link_TRANS : angle 0.55032 / 0.31 ( 15) *********************** 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 178 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8343 (OUTLIER) cc_final: 0.7791 (t60) REVERT: A 259 TYR cc_start: 0.7989 (m-80) cc_final: 0.7549 (m-80) REVERT: A 272 ARG cc_start: 0.6915 (ptp-170) cc_final: 0.4612 (mmt180) REVERT: A 325 TRP cc_start: 0.7560 (t60) cc_final: 0.7047 (t-100) REVERT: A 348 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7944 (ptt90) REVERT: A 349 LEU cc_start: 0.8743 (tp) cc_final: 0.8286 (tt) REVERT: A 424 GLU cc_start: 0.8242 (tp30) cc_final: 0.7438 (tm-30) REVERT: B 190 TRP cc_start: 0.5058 (t-100) cc_final: 0.4530 (t60) REVERT: B 308 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 353 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8229 (pt) REVERT: B 528 ASP cc_start: 0.8475 (t0) cc_final: 0.8265 (m-30) REVERT: B 596 LEU cc_start: 0.9224 (tp) cc_final: 0.8875 (tt) REVERT: C 81 LYS cc_start: 0.8801 (tppt) cc_final: 0.8513 (mmtt) REVERT: C 89 ASP cc_start: 0.8049 (m-30) cc_final: 0.7005 (m-30) REVERT: C 176 GLN cc_start: 0.8286 (tt0) cc_final: 0.7148 (pp30) REVERT: C 214 LYS cc_start: 0.8073 (tttm) cc_final: 0.7688 (tttp) REVERT: D 17 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 151 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: D 156 ILE cc_start: 0.5440 (mt) cc_final: 0.5184 (mt) outliers start: 35 outliers final: 28 residues processed: 169 average time/residue: 0.0804 time to fit residues: 19.5241 Evaluate side-chains 165 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 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 567 LEU Chi-restraints excluded: chain C residue 11 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 C residue 200 CYS 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 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119986 restraints weight = 14713.378| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.35 r_work: 0.3262 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10204 Z= 0.126 Angle : 0.596 9.848 13956 Z= 0.286 Chirality : 0.041 0.318 1656 Planarity : 0.005 0.075 1711 Dihedral : 4.808 44.991 1402 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.65 % Allowed : 15.75 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.23), residues: 1197 helix: -0.81 (0.23), residues: 458 sheet: -0.36 (0.38), residues: 183 loop : -1.65 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 613 TYR 0.014 0.001 TYR A 318 PHE 0.014 0.001 PHE A 336 TRP 0.009 0.001 TRP D 169 HIS 0.003 0.000 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10190) covalent geometry : angle 0.59330 / 0.29 (13918) SS BOND : bond 0.00357 / 0.16 ( 4) SS BOND : angle 1.66860 / 0.87 ( 8) hydrogen bonds : bond 0.03345 / 2.18 ( 333) hydrogen bonds : angle 4.66302 / 3.26 ( 978) link_BETA1-4 : bond 0.00290 / 0.15 ( 1) link_BETA1-4 : angle 0.95565 / 0.46 ( 3) link_NAG-ASN : bond 0.00349 / 0.15 ( 4) link_NAG-ASN : angle 1.43834 / 0.65 ( 12) link_TRANS : bond 0.00164 / 0.07 ( 5) link_TRANS : angle 0.48893 / 0.27 ( 15) *********************** 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 184 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7749 (t60) REVERT: A 155 TYR cc_start: 0.9166 (m-80) cc_final: 0.8305 (m-80) REVERT: A 259 TYR cc_start: 0.8046 (m-80) cc_final: 0.7644 (m-80) REVERT: A 272 ARG cc_start: 0.6964 (ptp-170) cc_final: 0.4594 (mmt180) REVERT: A 325 TRP cc_start: 0.7523 (t60) cc_final: 0.7020 (t-100) REVERT: A 348 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.7945 (ptt90) REVERT: A 349 LEU cc_start: 0.8717 (tp) cc_final: 0.8243 (tt) REVERT: A 424 GLU cc_start: 0.8251 (tp30) cc_final: 0.7469 (tm-30) REVERT: B 190 TRP cc_start: 0.5356 (t-100) cc_final: 0.4605 (t60) REVERT: B 274 GLN cc_start: 0.8300 (mt0) cc_final: 0.7980 (mt0) REVERT: B 308 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 353 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8234 (pt) REVERT: C 81 LYS cc_start: 0.8789 (tppt) cc_final: 0.8466 (mmtt) REVERT: C 89 ASP cc_start: 0.8033 (m-30) cc_final: 0.6939 (m-30) REVERT: C 176 GLN cc_start: 0.8216 (tt0) cc_final: 0.7127 (pp30) REVERT: C 214 LYS cc_start: 0.8057 (tttm) cc_final: 0.7581 (tttp) REVERT: D 151 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8303 (m-40) REVERT: D 156 ILE cc_start: 0.5396 (mt) cc_final: 0.5165 (mt) outliers start: 38 outliers final: 30 residues processed: 172 average time/residue: 0.0787 time to fit residues: 19.4130 Evaluate side-chains 171 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 194 LEU Chi-restraints excluded: chain B residue 203 ILE 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 C residue 11 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 529 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 = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119470 restraints weight = 14701.884| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.40 r_work: 0.3246 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10204 Z= 0.150 Angle : 0.622 8.850 13956 Z= 0.298 Chirality : 0.042 0.315 1656 Planarity : 0.005 0.076 1711 Dihedral : 4.859 45.442 1402 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.03 % Allowed : 15.75 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1197 helix: -0.66 (0.24), residues: 459 sheet: -0.32 (0.37), residues: 190 loop : -1.66 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 613 TYR 0.015 0.001 TYR A 318 PHE 0.013 0.001 PHE A 336 TRP 0.009 0.001 TRP D 169 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (10190) covalent geometry : angle 0.61920 / 0.30 (13918) SS BOND : bond 0.00336 / 0.16 ( 4) SS BOND : angle 1.58373 / 0.82 ( 8) hydrogen bonds : bond 0.03415 / 2.25 ( 333) hydrogen bonds : angle 4.65204 / 3.25 ( 978) link_BETA1-4 : bond 0.00326 / 0.17 ( 1) link_BETA1-4 : angle 1.05497 / 0.51 ( 3) link_NAG-ASN : bond 0.00305 / 0.13 ( 4) link_NAG-ASN : angle 1.52934 / 0.69 ( 12) link_TRANS : bond 0.00205 / 0.09 ( 5) link_TRANS : angle 0.59129 / 0.33 ( 15) *********************** 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 181 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7724 (t60) REVERT: A 155 TYR cc_start: 0.9129 (m-80) cc_final: 0.8516 (m-80) REVERT: A 259 TYR cc_start: 0.7898 (m-80) cc_final: 0.7508 (m-80) REVERT: A 272 ARG cc_start: 0.6976 (ptp-170) cc_final: 0.4618 (mmt180) REVERT: A 325 TRP cc_start: 0.7479 (t60) cc_final: 0.6940 (t-100) REVERT: A 348 ARG cc_start: 0.8263 (ptm-80) cc_final: 0.7840 (ptt90) REVERT: A 349 LEU cc_start: 0.8712 (tp) cc_final: 0.8276 (tt) REVERT: A 424 GLU cc_start: 0.8115 (tp30) cc_final: 0.7493 (tm-30) REVERT: B 190 TRP cc_start: 0.5273 (t-100) cc_final: 0.4570 (t60) REVERT: B 274 GLN cc_start: 0.8168 (mt0) cc_final: 0.7914 (mt0) REVERT: B 308 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 353 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8180 (pt) REVERT: C 89 ASP cc_start: 0.8048 (m-30) cc_final: 0.7150 (m-30) REVERT: C 176 GLN cc_start: 0.8141 (tt0) cc_final: 0.7083 (pp30) REVERT: C 201 ASN cc_start: 0.7061 (p0) cc_final: 0.6597 (p0) REVERT: C 214 LYS cc_start: 0.8196 (tttm) cc_final: 0.7707 (tttp) REVERT: D 17 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 151 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: D 156 ILE cc_start: 0.5427 (mt) cc_final: 0.5174 (mt) outliers start: 42 outliers final: 33 residues processed: 169 average time/residue: 0.0817 time to fit residues: 20.0521 Evaluate side-chains 174 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 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 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 89 LEU Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116486 restraints weight = 14763.770| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.39 r_work: 0.3216 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10204 Z= 0.211 Angle : 0.674 9.591 13956 Z= 0.325 Chirality : 0.044 0.320 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.102 45.167 1402 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.84 % Allowed : 15.85 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1197 helix: -0.64 (0.24), residues: 458 sheet: -0.36 (0.37), residues: 191 loop : -1.66 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 613 TYR 0.017 0.002 TYR B 225 PHE 0.015 0.002 PHE C 151 TRP 0.012 0.001 TRP D 169 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (10190) covalent geometry : angle 0.67077 / 0.32 (13918) SS BOND : bond 0.00379 / 0.18 ( 4) SS BOND : angle 1.55311 / 0.81 ( 8) hydrogen bonds : bond 0.03726 / 2.47 ( 333) hydrogen bonds : angle 4.79292 / 3.34 ( 978) link_BETA1-4 : bond 0.00283 / 0.15 ( 1) link_BETA1-4 : angle 1.10834 / 0.53 ( 3) link_NAG-ASN : bond 0.00249 / 0.10 ( 4) link_NAG-ASN : angle 1.76110 / 0.79 ( 12) link_TRANS : bond 0.00296 / 0.13 ( 5) link_TRANS : angle 0.77849 / 0.43 ( 15) *********************** 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 181 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7831 (t60) REVERT: A 155 TYR cc_start: 0.9256 (m-80) cc_final: 0.8659 (m-80) REVERT: A 259 TYR cc_start: 0.8112 (m-80) cc_final: 0.7658 (m-80) REVERT: A 272 ARG cc_start: 0.6987 (ptp-170) cc_final: 0.4680 (mmt180) REVERT: A 325 TRP cc_start: 0.7628 (t60) cc_final: 0.7014 (t-100) REVERT: A 348 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8020 (ptt90) REVERT: A 349 LEU cc_start: 0.8788 (tp) cc_final: 0.8353 (tt) REVERT: A 424 GLU cc_start: 0.8270 (tp30) cc_final: 0.7547 (tm-30) REVERT: B 190 TRP cc_start: 0.5613 (t-100) cc_final: 0.4575 (t60) REVERT: B 274 GLN cc_start: 0.8427 (mt0) cc_final: 0.8117 (mt0) REVERT: B 308 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8605 (mm) REVERT: B 353 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8361 (pt) REVERT: B 596 LEU cc_start: 0.9298 (tt) cc_final: 0.9047 (tt) REVERT: C 89 ASP cc_start: 0.8223 (m-30) cc_final: 0.6883 (m-30) REVERT: C 176 GLN cc_start: 0.8264 (tt0) cc_final: 0.7095 (pp30) REVERT: C 201 ASN cc_start: 0.7283 (p0) cc_final: 0.6837 (p0) REVERT: C 214 LYS cc_start: 0.8099 (tttm) cc_final: 0.7661 (tttp) REVERT: D 17 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8142 (mt-10) REVERT: D 151 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8333 (m-40) REVERT: D 156 ILE cc_start: 0.5472 (mt) cc_final: 0.5211 (mt) outliers start: 40 outliers final: 33 residues processed: 168 average time/residue: 0.0853 time to fit residues: 20.6992 Evaluate side-chains 173 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 372 THR Chi-restraints excluded: chain A residue 378 VAL 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 194 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.6980 chunk 41 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 49 optimal weight: 0.5980 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126690 restraints weight = 14552.622| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.34 r_work: 0.3225 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10204 Z= 0.104 Angle : 0.596 10.274 13956 Z= 0.282 Chirality : 0.041 0.312 1656 Planarity : 0.005 0.076 1711 Dihedral : 4.773 46.417 1402 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.98 % Allowed : 16.62 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1197 helix: -0.27 (0.24), residues: 457 sheet: -0.21 (0.39), residues: 183 loop : -1.58 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 613 TYR 0.017 0.001 TYR A 318 PHE 0.015 0.001 PHE A 336 TRP 0.011 0.001 TRP B 190 HIS 0.002 0.000 HIS B 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (10190) covalent geometry : angle 0.59466 / 0.28 (13918) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 1.51469 / 0.78 ( 8) hydrogen bonds : bond 0.03027 / 1.99 ( 333) hydrogen bonds : angle 4.54138 / 3.20 ( 978) link_BETA1-4 : bond 0.00137 / 0.07 ( 1) link_BETA1-4 : angle 0.80258 / 0.41 ( 3) link_NAG-ASN : bond 0.00412 / 0.19 ( 4) link_NAG-ASN : angle 1.20950 / 0.58 ( 12) link_TRANS : bond 0.00128 / 0.06 ( 5) link_TRANS : angle 0.36573 / 0.20 ( 15) *********************** 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 181 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8301 (OUTLIER) cc_final: 0.7744 (t60) REVERT: A 259 TYR cc_start: 0.8123 (m-80) cc_final: 0.7744 (m-80) REVERT: A 272 ARG cc_start: 0.7010 (ptp-170) cc_final: 0.4599 (mmt180) REVERT: A 325 TRP cc_start: 0.7486 (t60) cc_final: 0.6869 (t-100) REVERT: A 348 ARG cc_start: 0.8351 (ptm-80) cc_final: 0.7960 (ptt90) REVERT: A 349 LEU cc_start: 0.8701 (tp) cc_final: 0.8331 (tt) REVERT: A 419 ARG cc_start: 0.7340 (mmp-170) cc_final: 0.7098 (mmm160) REVERT: A 424 GLU cc_start: 0.8160 (tp30) cc_final: 0.7574 (tm-30) REVERT: B 190 TRP cc_start: 0.5406 (t-100) cc_final: 0.4988 (t60) REVERT: B 274 GLN cc_start: 0.8075 (mt0) cc_final: 0.7859 (mt0) REVERT: B 353 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8157 (pt) REVERT: B 596 LEU cc_start: 0.9203 (tt) cc_final: 0.8996 (tt) REVERT: C 89 ASP cc_start: 0.7835 (m-30) cc_final: 0.7198 (m-30) REVERT: C 176 GLN cc_start: 0.8290 (tt0) cc_final: 0.7274 (pp30) REVERT: C 201 ASN cc_start: 0.7181 (p0) cc_final: 0.6840 (p0) REVERT: C 214 LYS cc_start: 0.8029 (tttm) cc_final: 0.7708 (tttp) REVERT: D 17 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 129 GLU cc_start: 0.7546 (tt0) cc_final: 0.6924 (mp0) REVERT: D 156 ILE cc_start: 0.5415 (mt) cc_final: 0.5197 (mt) outliers start: 31 outliers final: 23 residues processed: 169 average time/residue: 0.0853 time to fit residues: 20.6281 Evaluate side-chains 160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 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 407 ASP 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 95 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119908 restraints weight = 14540.066| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.34 r_work: 0.3277 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3172 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= 0.122 Angle : 0.626 9.825 13956 Z= 0.298 Chirality : 0.041 0.305 1656 Planarity : 0.005 0.076 1711 Dihedral : 4.787 46.346 1402 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.50 % Allowed : 17.77 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1197 helix: -0.21 (0.24), residues: 459 sheet: -0.17 (0.39), residues: 183 loop : -1.52 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 613 TYR 0.014 0.001 TYR A 318 PHE 0.014 0.001 PHE A 336 TRP 0.009 0.001 TRP B 218 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10190) covalent geometry : angle 0.62312 / 0.30 (13918) SS BOND : bond 0.00237 / 0.11 ( 4) SS BOND : angle 2.23965 / 1.19 ( 8) hydrogen bonds : bond 0.03154 / 2.07 ( 333) hydrogen bonds : angle 4.51811 / 3.18 ( 978) link_BETA1-4 : bond 0.00312 / 0.16 ( 1) link_BETA1-4 : angle 0.93639 / 0.46 ( 3) link_NAG-ASN : bond 0.00329 / 0.14 ( 4) link_NAG-ASN : angle 1.33889 / 0.62 ( 12) link_TRANS : bond 0.00178 / 0.07 ( 5) link_TRANS : angle 0.46196 / 0.26 ( 15) ********************** 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 164 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7540 (tp30) REVERT: A 134 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7794 (t60) REVERT: A 259 TYR cc_start: 0.8272 (m-80) cc_final: 0.7835 (m-80) REVERT: A 272 ARG cc_start: 0.7069 (ptp-170) cc_final: 0.4867 (mmt180) REVERT: A 314 ASP cc_start: 0.7950 (m-30) cc_final: 0.7729 (m-30) REVERT: A 325 TRP cc_start: 0.7507 (t60) cc_final: 0.6803 (t-100) REVERT: A 348 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7976 (ptt90) REVERT: A 349 LEU cc_start: 0.8719 (tp) cc_final: 0.8379 (tt) REVERT: A 405 TRP cc_start: 0.8579 (m100) cc_final: 0.8364 (m100) REVERT: A 424 GLU cc_start: 0.8304 (tp30) cc_final: 0.7665 (tm-30) REVERT: B 190 TRP cc_start: 0.5796 (t-100) cc_final: 0.5182 (t60) REVERT: B 274 GLN cc_start: 0.8267 (mt0) cc_final: 0.8003 (mt0) REVERT: B 353 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8256 (pt) REVERT: B 596 LEU cc_start: 0.9249 (tt) cc_final: 0.9010 (tt) REVERT: C 89 ASP cc_start: 0.7993 (m-30) cc_final: 0.7067 (m-30) REVERT: C 176 GLN cc_start: 0.8328 (tt0) cc_final: 0.7217 (pp30) REVERT: C 201 ASN cc_start: 0.7177 (p0) cc_final: 0.6852 (p0) REVERT: C 214 LYS cc_start: 0.8058 (tttm) cc_final: 0.7577 (tttp) REVERT: D 17 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 129 GLU cc_start: 0.7557 (tt0) cc_final: 0.6901 (mp0) REVERT: D 156 ILE cc_start: 0.5395 (mt) cc_final: 0.5138 (mt) outliers start: 26 outliers final: 23 residues processed: 154 average time/residue: 0.0872 time to fit residues: 19.3772 Evaluate side-chains 157 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 390 SER 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 460 ILE Chi-restraints excluded: chain B residue 221 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 C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116342 restraints weight = 14780.293| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.31 r_work: 0.3253 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10204 Z= 0.162 Angle : 0.656 10.019 13956 Z= 0.314 Chirality : 0.043 0.306 1656 Planarity : 0.005 0.075 1711 Dihedral : 4.911 45.946 1402 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 17.96 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1197 helix: -0.24 (0.24), residues: 457 sheet: -0.28 (0.39), residues: 183 loop : -1.51 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 419 TYR 0.014 0.001 TYR A 318 PHE 0.013 0.001 PHE A 336 TRP 0.015 0.001 TRP D 169 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10190) covalent geometry : angle 0.65324 / 0.31 (13918) SS BOND : bond 0.00329 / 0.16 ( 4) SS BOND : angle 2.18253 / 1.18 ( 8) hydrogen bonds : bond 0.03380 / 2.24 ( 333) hydrogen bonds : angle 4.59835 / 3.23 ( 978) link_BETA1-4 : bond 0.00093 / 0.05 ( 1) link_BETA1-4 : angle 0.90093 / 0.44 ( 3) link_NAG-ASN : bond 0.00288 / 0.12 ( 4) link_NAG-ASN : angle 1.47677 / 0.67 ( 12) link_TRANS : bond 0.00222 / 0.10 ( 5) link_TRANS : angle 0.62298 / 0.34 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.29 seconds wall clock time: 42 minutes 52.87 seconds (2572.87 seconds total)