Starting phenix.real_space_refine on Fri Feb 14 12:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.map" model { file = "/net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jmq_9849/02_2025/6jmq_9849.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6468 2.51 5 N 1606 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3101 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3520 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 212 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 3, 'TRANS': 26} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 140 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 340 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 834 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 162 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 486 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 119} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.51, per 1000 atoms: 0.65 Number of scatterers: 9950 At special positions: 0 Unit cell: (130.634, 83.979, 154.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1841 8.00 N 1606 7.00 C 6468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 704 " - " ASN B 424 " " NAG B 705 " - " ASN B 506 " " NAG B 706 " - " ASN B 365 " " NAG E 1 " - " ASN B 381 " TRANS " UNK C 31 " - " THR C 30 " " UNK C 50 " - " GLY C 49 " " UNK C 98 " - " ARG C 97 " " UNK D 24 " - " CYS D 23 " " UNK D 95 " - " CYS D 94 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 42.4% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.738A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.060A pdb=" N ILE A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.060A pdb=" N GLY A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 113 removed outlier: 3.606A pdb=" N VAL A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.110A pdb=" N TYR A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.600A pdb=" N ILE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.513A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 189 removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.595A pdb=" N ALA A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.514A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.708A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.014A pdb=" N SER A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 265 removed outlier: 3.668A pdb=" N THR A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.535A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.029A pdb=" N VAL A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.547A pdb=" N ASP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.600A pdb=" N ILE A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.593A pdb=" N ARG A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.537A pdb=" N LEU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.736A pdb=" N VAL A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 454 removed outlier: 4.484A pdb=" N VAL A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 4.311A pdb=" N CYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 removed outlier: 4.030A pdb=" N VAL A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 4.224A pdb=" N LEU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 235 removed outlier: 3.966A pdb=" N GLN B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.865A pdb=" N LYS B 245 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.554A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.999A pdb=" N VAL B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 removed outlier: 3.517A pdb=" N LEU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.842A pdb=" N ILE B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 460 removed outlier: 3.649A pdb=" N LEU B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 removed outlier: 4.355A pdb=" N GLU B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.694A pdb=" N ASP B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'C' and resid 28 through 32 No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.963A pdb=" N UNK C 64 " --> pdb=" O UNK C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.974A pdb=" N THR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.535A pdb=" N SER D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.616A pdb=" N GLU D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.684A pdb=" N PHE B 466 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.778A pdb=" N GLN B 279 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 307 removed outlier: 6.648A pdb=" N LEU B 306 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 345 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY B 379 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 399 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.584A pdb=" N HIS B 556 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 542 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY B 621 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER B 598 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 623 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.639A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 21 removed outlier: 3.586A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 129 removed outlier: 6.160A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 129 removed outlier: 6.160A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 174 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.545A pdb=" N THR C 158 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 200 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 4 through 6 current: chain 'D' and resid 20 through 25 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.959A pdb=" N LEU D 11 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.560A pdb=" N ASN D 143 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA D 136 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 138 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR D 179 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 182 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 168 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.873A pdb=" N TRP D 154 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 198 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 215 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3051 1.34 - 1.46: 1941 1.46 - 1.57: 5149 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10190 Sorted by residual: bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C SER D 7 " pdb=" N PRO D 8 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.76e+01 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.333 1.369 -0.035 1.01e-02 9.80e+03 1.22e+01 bond pdb=" C ARG A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" C1 NAG B 706 " pdb=" O5 NAG B 706 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 10185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13403 2.21 - 4.41: 438 4.41 - 6.62: 52 6.62 - 8.83: 18 8.83 - 11.03: 7 Bond angle restraints: 13918 Sorted by residual: angle pdb=" C UNK D 56 " pdb=" N UNK D 57 " pdb=" CA UNK D 57 " ideal model delta sigma weight residual 121.70 131.80 -10.10 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N THR A 71 " pdb=" CA THR A 71 " pdb=" C THR A 71 " ideal model delta sigma weight residual 109.81 120.57 -10.76 2.21e+00 2.05e-01 2.37e+01 angle pdb=" C ILE D 156 " pdb=" N ASP D 157 " pdb=" CA ASP D 157 " ideal model delta sigma weight residual 122.46 128.46 -6.00 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C SER A 126 " pdb=" N LEU A 127 " pdb=" CA LEU A 127 " ideal model delta sigma weight residual 120.06 125.12 -5.06 1.19e+00 7.06e-01 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" C LEU B 261 " ideal model delta sigma weight residual 110.35 116.09 -5.74 1.40e+00 5.10e-01 1.68e+01 ... (remaining 13913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 5866 21.25 - 42.51: 391 42.51 - 63.76: 50 63.76 - 85.01: 12 85.01 - 106.27: 3 Dihedral angle restraints: 6322 sinusoidal: 2614 harmonic: 3708 Sorted by residual: dihedral pdb=" CA ARG A 427 " pdb=" C ARG A 427 " pdb=" N PRO A 428 " pdb=" CA PRO A 428 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA A 118 " pdb=" C ALA A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 259 " pdb=" C LEU B 259 " pdb=" N VAL B 260 " pdb=" CA VAL B 260 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1220 0.051 - 0.102: 324 0.102 - 0.153: 91 0.153 - 0.204: 17 0.204 - 0.255: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 424 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.56e+00 ... (remaining 1653 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 372 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 373 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 469 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 470 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 158 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO A 159 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.043 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2958 2.81 - 3.34: 8290 3.34 - 3.86: 15542 3.86 - 4.38: 17629 4.38 - 4.90: 30945 Nonbonded interactions: 75364 Sorted by model distance: nonbonded pdb=" OG SER B 535 " pdb=" O GLU B 561 " model vdw 2.293 3.040 nonbonded pdb=" O TYR B 250 " pdb=" OG SER B 253 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG A 419 " pdb=" OE2 GLU A 426 " model vdw 2.358 3.120 nonbonded pdb=" O ILE A 139 " pdb=" OG SER A 143 " model vdw 2.361 3.040 nonbonded pdb=" O TRP B 363 " pdb=" OG1 THR B 367 " model vdw 2.372 3.040 ... (remaining 75359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10190 Z= 0.329 Angle : 0.958 11.034 13918 Z= 0.523 Chirality : 0.052 0.255 1656 Planarity : 0.007 0.084 1711 Dihedral : 14.029 106.266 3905 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 0.29 % Allowed : 7.40 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.18), residues: 1197 helix: -4.70 (0.09), residues: 437 sheet: -1.52 (0.39), residues: 159 loop : -2.72 (0.20), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 190 HIS 0.004 0.001 HIS D 204 PHE 0.016 0.002 PHE B 551 TYR 0.019 0.002 TYR B 453 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 111 SER cc_start: 0.7608 (m) cc_final: 0.7130 (p) REVERT: A 134 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7734 (t60) REVERT: A 259 TYR cc_start: 0.7910 (m-80) cc_final: 0.7371 (m-80) REVERT: A 272 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6789 (ptp-170) REVERT: A 325 TRP cc_start: 0.7324 (t60) cc_final: 0.7116 (t-100) REVERT: A 326 ILE cc_start: 0.8628 (tt) cc_final: 0.8369 (tt) REVERT: A 407 CYS cc_start: 0.7519 (m) cc_final: 0.7249 (m) REVERT: A 424 GLU cc_start: 0.7617 (tp30) cc_final: 0.6839 (tm-30) REVERT: B 325 THR cc_start: 0.9133 (p) cc_final: 0.8921 (t) REVERT: B 370 PHE cc_start: 0.8066 (t80) cc_final: 0.7462 (t80) REVERT: B 528 ASP cc_start: 0.8021 (t0) cc_final: 0.7815 (m-30) REVERT: B 607 SER cc_start: 0.8640 (p) cc_final: 0.8029 (m) REVERT: B 625 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7972 (mtm110) REVERT: C 89 ASP cc_start: 0.8085 (m-30) cc_final: 0.7014 (m-30) REVERT: D 6 GLN cc_start: 0.8495 (tt0) cc_final: 0.8218 (mt0) REVERT: D 42 TYR cc_start: 0.9058 (m-80) cc_final: 0.8823 (m-80) REVERT: D 156 ILE cc_start: 0.6044 (mt) cc_final: 0.5819 (mt) REVERT: D 176 ASP cc_start: 0.8609 (p0) cc_final: 0.7738 (p0) REVERT: D 201 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7460 (mm-30) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.2382 time to fit residues: 70.1082 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 : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 186 ASN A 218 GLN A 293 ASN B 267 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS B 560 ASN C 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125405 restraints weight = 14686.189| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.64 r_work: 0.3191 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10190 Z= 0.228 Angle : 0.657 9.407 13918 Z= 0.330 Chirality : 0.042 0.209 1656 Planarity : 0.006 0.083 1711 Dihedral : 7.723 89.160 1787 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.83 % Allowed : 12.78 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.20), residues: 1197 helix: -3.10 (0.18), residues: 444 sheet: -1.03 (0.36), residues: 180 loop : -2.26 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 405 HIS 0.002 0.001 HIS C 204 PHE 0.016 0.001 PHE B 551 TYR 0.011 0.001 TYR B 225 ARG 0.005 0.001 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.161 Fit side-chains REVERT: A 54 ASN cc_start: 0.7231 (t160) cc_final: 0.6526 (m110) REVERT: A 134 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7904 (t60) REVERT: A 155 TYR cc_start: 0.9216 (m-80) cc_final: 0.8947 (m-80) REVERT: A 243 ILE cc_start: 0.7971 (tp) cc_final: 0.7712 (tp) REVERT: A 259 TYR cc_start: 0.8173 (m-80) cc_final: 0.7564 (m-80) REVERT: A 272 ARG cc_start: 0.7100 (ptp-170) cc_final: 0.4724 (mmt180) REVERT: A 325 TRP cc_start: 0.7441 (t60) cc_final: 0.7103 (t-100) REVERT: A 326 ILE cc_start: 0.8746 (tt) cc_final: 0.8498 (tt) REVERT: A 348 ARG cc_start: 0.8207 (ptm-80) cc_final: 0.7800 (ptt90) REVERT: A 349 LEU cc_start: 0.8832 (tp) cc_final: 0.8455 (tt) REVERT: A 424 GLU cc_start: 0.8134 (tp30) cc_final: 0.7033 (tm-30) REVERT: B 190 TRP cc_start: 0.5373 (t-100) cc_final: 0.4085 (t60) REVERT: B 231 GLN cc_start: 0.8524 (tp40) cc_final: 0.8289 (tp-100) REVERT: B 255 LYS cc_start: 0.9142 (mttm) cc_final: 0.8812 (mtmm) REVERT: C 89 ASP cc_start: 0.8115 (m-30) cc_final: 0.7031 (m-30) REVERT: C 214 LYS cc_start: 0.8262 (tttm) cc_final: 0.7577 (tttp) REVERT: D 156 ILE cc_start: 0.5518 (mt) cc_final: 0.5218 (mt) outliers start: 19 outliers final: 15 residues processed: 174 average time/residue: 0.2453 time to fit residues: 59.3600 Evaluate side-chains 157 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.0010 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118096 restraints weight = 14680.023| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.69 r_work: 0.3242 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10190 Z= 0.227 Angle : 0.635 8.477 13918 Z= 0.310 Chirality : 0.042 0.228 1656 Planarity : 0.005 0.081 1711 Dihedral : 7.266 87.065 1787 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.69 % Allowed : 14.99 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1197 helix: -2.19 (0.21), residues: 453 sheet: -0.66 (0.37), residues: 180 loop : -2.00 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 190 HIS 0.002 0.001 HIS C 204 PHE 0.016 0.001 PHE A 336 TYR 0.013 0.001 TYR A 318 ARG 0.003 0.000 ARG B 625 *********************** 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 178 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.341 Fit side-chains REVERT: A 134 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7812 (t60) REVERT: A 272 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.4653 (mmt180) REVERT: A 325 TRP cc_start: 0.7524 (t60) cc_final: 0.7062 (t-100) REVERT: A 348 ARG cc_start: 0.8189 (ptm-80) cc_final: 0.7766 (ptt90) REVERT: A 349 LEU cc_start: 0.8799 (tp) cc_final: 0.8362 (tt) REVERT: A 424 GLU cc_start: 0.8165 (tp30) cc_final: 0.7149 (tm-30) REVERT: B 190 TRP cc_start: 0.5198 (t-100) cc_final: 0.4321 (t60) REVERT: B 231 GLN cc_start: 0.8555 (tp40) cc_final: 0.8314 (tp-100) REVERT: B 353 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8048 (pt) REVERT: B 372 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: B 528 ASP cc_start: 0.8290 (t0) cc_final: 0.7946 (m-30) REVERT: C 89 ASP cc_start: 0.8016 (m-30) cc_final: 0.6884 (m-30) REVERT: C 214 LYS cc_start: 0.8148 (tttm) cc_final: 0.7877 (tttp) REVERT: D 17 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 129 GLU cc_start: 0.7309 (tt0) cc_final: 0.6725 (mp0) REVERT: D 156 ILE cc_start: 0.5661 (mt) cc_final: 0.5403 (mt) REVERT: D 185 LEU cc_start: 0.7082 (mt) cc_final: 0.6752 (mt) outliers start: 28 outliers final: 18 residues processed: 167 average time/residue: 0.2269 time to fit residues: 53.1401 Evaluate side-chains 163 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 191 LEU Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 0.0770 chunk 73 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.157772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125431 restraints weight = 14490.942| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.32 r_work: 0.3206 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10190 Z= 0.203 Angle : 0.602 7.848 13918 Z= 0.293 Chirality : 0.042 0.222 1656 Planarity : 0.005 0.078 1711 Dihedral : 6.853 82.848 1787 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.55 % Allowed : 15.27 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1197 helix: -1.61 (0.22), residues: 456 sheet: -0.38 (0.39), residues: 173 loop : -1.88 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 190 HIS 0.002 0.001 HIS C 204 PHE 0.015 0.001 PHE A 336 TYR 0.011 0.001 TYR B 225 ARG 0.004 0.000 ARG B 613 *********************** 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 186 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.049 Fit side-chains REVERT: A 134 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7706 (t60) REVERT: A 259 TYR cc_start: 0.7657 (m-80) cc_final: 0.7237 (m-80) REVERT: A 272 ARG cc_start: 0.7214 (ptp-170) cc_final: 0.4817 (mmt180) REVERT: A 325 TRP cc_start: 0.7541 (t60) cc_final: 0.7165 (t-100) REVERT: A 348 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.7913 (ptt90) REVERT: A 349 LEU cc_start: 0.8787 (tp) cc_final: 0.8326 (tt) REVERT: A 424 GLU cc_start: 0.8152 (tp30) cc_final: 0.7283 (tm-30) REVERT: B 190 TRP cc_start: 0.5159 (t-100) cc_final: 0.4611 (t60) REVERT: B 353 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8079 (pt) REVERT: B 528 ASP cc_start: 0.8424 (t0) cc_final: 0.8213 (m-30) REVERT: C 81 LYS cc_start: 0.8796 (tppt) cc_final: 0.8506 (mmtt) REVERT: C 89 ASP cc_start: 0.8106 (m-30) cc_final: 0.7070 (m-30) REVERT: C 214 LYS cc_start: 0.8234 (tttm) cc_final: 0.7911 (tttp) REVERT: D 17 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8017 (mt-10) REVERT: D 129 GLU cc_start: 0.7422 (tt0) cc_final: 0.6843 (mp0) REVERT: D 151 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: D 156 ILE cc_start: 0.5615 (mt) cc_final: 0.5361 (mt) REVERT: D 185 LEU cc_start: 0.7308 (mt) cc_final: 0.7008 (mt) outliers start: 37 outliers final: 27 residues processed: 175 average time/residue: 0.2135 time to fit residues: 52.3908 Evaluate side-chains 169 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.159250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125991 restraints weight = 14593.528| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.51 r_work: 0.3218 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10190 Z= 0.160 Angle : 0.579 8.448 13918 Z= 0.278 Chirality : 0.041 0.213 1656 Planarity : 0.005 0.077 1711 Dihedral : 6.443 77.825 1787 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.46 % Allowed : 16.04 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.23), residues: 1197 helix: -1.07 (0.23), residues: 455 sheet: -0.25 (0.39), residues: 173 loop : -1.77 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 190 HIS 0.002 0.000 HIS C 204 PHE 0.015 0.001 PHE A 402 TYR 0.010 0.001 TYR A 155 ARG 0.005 0.000 ARG B 613 *********************** 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 192 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.167 Fit side-chains REVERT: A 134 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7730 (t60) REVERT: A 259 TYR cc_start: 0.7912 (m-80) cc_final: 0.7506 (m-80) REVERT: A 272 ARG cc_start: 0.6967 (ptp-170) cc_final: 0.4620 (mmt180) REVERT: A 317 ASN cc_start: 0.8053 (m-40) cc_final: 0.7593 (m-40) REVERT: A 325 TRP cc_start: 0.7453 (t60) cc_final: 0.7015 (t-100) REVERT: A 348 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.7979 (ptt90) REVERT: A 349 LEU cc_start: 0.8698 (tp) cc_final: 0.8252 (tt) REVERT: A 424 GLU cc_start: 0.8184 (tp30) cc_final: 0.7405 (tm-30) REVERT: B 190 TRP cc_start: 0.5089 (t-100) cc_final: 0.4820 (t60) REVERT: B 308 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8504 (mm) REVERT: B 353 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8095 (pt) REVERT: C 81 LYS cc_start: 0.8799 (tppt) cc_final: 0.8510 (mmtt) REVERT: C 89 ASP cc_start: 0.7957 (m-30) cc_final: 0.6970 (m-30) REVERT: C 176 GLN cc_start: 0.8262 (tt0) cc_final: 0.7192 (pp30) REVERT: C 214 LYS cc_start: 0.8150 (tttm) cc_final: 0.7624 (tttp) REVERT: D 17 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 129 GLU cc_start: 0.7401 (tt0) cc_final: 0.6807 (mp0) REVERT: D 151 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8162 (m-40) REVERT: D 185 LEU cc_start: 0.7422 (mt) cc_final: 0.7129 (mt) outliers start: 36 outliers final: 25 residues processed: 181 average time/residue: 0.2148 time to fit residues: 55.1687 Evaluate side-chains 169 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain 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 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 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 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120733 restraints weight = 14572.658| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.39 r_work: 0.3263 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10190 Z= 0.195 Angle : 0.605 9.100 13918 Z= 0.287 Chirality : 0.041 0.212 1656 Planarity : 0.005 0.075 1711 Dihedral : 6.550 75.426 1787 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.84 % Allowed : 16.14 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1197 helix: -0.78 (0.23), residues: 459 sheet: -0.42 (0.38), residues: 183 loop : -1.66 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.002 0.000 HIS C 204 PHE 0.014 0.001 PHE A 336 TYR 0.014 0.001 TYR A 318 ARG 0.005 0.000 ARG B 613 *********************** 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 187 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.095 Fit side-chains REVERT: A 134 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7679 (t60) REVERT: A 259 TYR cc_start: 0.7889 (m-80) cc_final: 0.7478 (m-80) REVERT: A 272 ARG cc_start: 0.6946 (ptp-170) cc_final: 0.4595 (mmt180) REVERT: A 317 ASN cc_start: 0.7922 (m-40) cc_final: 0.7571 (m-40) REVERT: A 325 TRP cc_start: 0.7470 (t60) cc_final: 0.7025 (t-100) REVERT: A 348 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.7913 (ptt90) REVERT: A 349 LEU cc_start: 0.8717 (tp) cc_final: 0.8284 (tt) REVERT: A 424 GLU cc_start: 0.8134 (tp30) cc_final: 0.7426 (tm-30) REVERT: B 190 TRP cc_start: 0.5101 (t-100) cc_final: 0.4798 (t60) REVERT: B 308 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 353 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8115 (pt) REVERT: B 528 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: C 81 LYS cc_start: 0.8738 (tppt) cc_final: 0.8393 (mmtt) REVERT: C 89 ASP cc_start: 0.8045 (m-30) cc_final: 0.7010 (m-30) REVERT: C 176 GLN cc_start: 0.8174 (tt0) cc_final: 0.7134 (pp30) REVERT: C 214 LYS cc_start: 0.8115 (tttm) cc_final: 0.7592 (tttp) REVERT: D 129 GLU cc_start: 0.7307 (tt0) cc_final: 0.6747 (mp0) REVERT: D 151 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: D 185 LEU cc_start: 0.7576 (mt) cc_final: 0.7210 (mt) outliers start: 40 outliers final: 29 residues processed: 173 average time/residue: 0.2224 time to fit residues: 55.6335 Evaluate side-chains 176 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 251 LEU Chi-restraints excluded: chain B residue 308 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 528 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 17 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114131 restraints weight = 14870.009| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.41 r_work: 0.3219 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10190 Z= 0.295 Angle : 0.661 8.988 13918 Z= 0.316 Chirality : 0.044 0.219 1656 Planarity : 0.005 0.075 1711 Dihedral : 6.619 73.720 1787 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.84 % Allowed : 16.14 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.23), residues: 1197 helix: -0.71 (0.23), residues: 458 sheet: -0.34 (0.37), residues: 190 loop : -1.70 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS C 204 PHE 0.014 0.001 PHE C 151 TYR 0.015 0.002 TYR A 318 ARG 0.006 0.000 ARG B 613 *********************** 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 177 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.970 Fit side-chains REVERT: A 134 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7776 (t60) REVERT: A 259 TYR cc_start: 0.8049 (m-80) cc_final: 0.7595 (m-80) REVERT: A 272 ARG cc_start: 0.6978 (ptp-170) cc_final: 0.4678 (mmt180) REVERT: A 325 TRP cc_start: 0.7545 (t60) cc_final: 0.7082 (t-100) REVERT: A 348 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7962 (ptt90) REVERT: A 349 LEU cc_start: 0.8726 (tp) cc_final: 0.8283 (tt) REVERT: A 424 GLU cc_start: 0.8278 (tp30) cc_final: 0.7533 (tm-30) REVERT: B 190 TRP cc_start: 0.5550 (t-100) cc_final: 0.4679 (t60) REVERT: B 274 GLN cc_start: 0.8408 (mt0) cc_final: 0.8103 (mt0) REVERT: B 308 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 353 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8316 (pt) REVERT: B 528 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: C 81 LYS cc_start: 0.8713 (tppt) cc_final: 0.8388 (mmtt) REVERT: C 89 ASP cc_start: 0.8238 (m-30) cc_final: 0.6994 (m-30) REVERT: C 176 GLN cc_start: 0.8235 (tt0) cc_final: 0.7084 (pp30) REVERT: C 201 ASN cc_start: 0.7120 (p0) cc_final: 0.6723 (p0) REVERT: C 214 LYS cc_start: 0.8099 (tttm) cc_final: 0.7551 (tttp) REVERT: D 17 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8215 (mt-10) REVERT: D 129 GLU cc_start: 0.7491 (tt0) cc_final: 0.6849 (mp0) REVERT: D 151 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8314 (m-40) REVERT: D 185 LEU cc_start: 0.7691 (mt) cc_final: 0.7290 (mt) outliers start: 40 outliers final: 31 residues processed: 164 average time/residue: 0.2199 time to fit residues: 51.0396 Evaluate side-chains 170 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 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 528 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 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 188 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116146 restraints weight = 14805.598| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.62 r_work: 0.3216 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10190 Z= 0.229 Angle : 0.626 9.303 13918 Z= 0.298 Chirality : 0.042 0.192 1656 Planarity : 0.005 0.075 1711 Dihedral : 6.352 67.297 1787 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.55 % Allowed : 16.91 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1197 helix: -0.53 (0.24), residues: 458 sheet: -0.27 (0.38), residues: 190 loop : -1.64 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.003 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.015 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 *********************** 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: 37 poor density : 144 time to evaluate : 1.259 Fit side-chains REVERT: A 134 TRP cc_start: 0.8416 (OUTLIER) cc_final: 0.7738 (t60) REVERT: A 259 TYR cc_start: 0.7980 (m-80) cc_final: 0.7560 (m-80) REVERT: A 272 ARG cc_start: 0.6930 (ptp-170) cc_final: 0.4610 (mmt180) REVERT: A 317 ASN cc_start: 0.7946 (m-40) cc_final: 0.7675 (m-40) REVERT: A 325 TRP cc_start: 0.7552 (t60) cc_final: 0.7018 (t-100) REVERT: A 348 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.7940 (ptt90) REVERT: A 349 LEU cc_start: 0.8739 (tp) cc_final: 0.8329 (tt) REVERT: A 424 GLU cc_start: 0.8145 (tp30) cc_final: 0.7514 (tm-30) REVERT: B 190 TRP cc_start: 0.5410 (t-100) cc_final: 0.4790 (t60) REVERT: B 274 GLN cc_start: 0.8278 (mt0) cc_final: 0.8005 (mt0) REVERT: B 308 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8411 (mm) REVERT: B 353 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8194 (pt) REVERT: B 528 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: C 81 LYS cc_start: 0.8659 (tppt) cc_final: 0.8294 (mmtt) REVERT: C 89 ASP cc_start: 0.8058 (m-30) cc_final: 0.6925 (m-30) REVERT: C 176 GLN cc_start: 0.8168 (tt0) cc_final: 0.7059 (pp30) REVERT: C 201 ASN cc_start: 0.7247 (p0) cc_final: 0.6724 (p0) REVERT: C 214 LYS cc_start: 0.8041 (tttm) cc_final: 0.7712 (tttp) REVERT: D 17 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 129 GLU cc_start: 0.7443 (tt0) cc_final: 0.6850 (mp0) REVERT: D 151 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8168 (m-40) REVERT: D 185 LEU cc_start: 0.7621 (mt) cc_final: 0.7221 (mt) outliers start: 37 outliers final: 31 residues processed: 168 average time/residue: 0.2306 time to fit residues: 54.4705 Evaluate side-chains 173 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 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 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 528 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 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 1 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126652 restraints weight = 14720.336| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.44 r_work: 0.3200 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10190 Z= 0.166 Angle : 0.597 9.719 13918 Z= 0.281 Chirality : 0.040 0.162 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.934 59.288 1787 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.36 % Allowed : 17.48 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1197 helix: -0.26 (0.24), residues: 457 sheet: -0.24 (0.39), residues: 185 loop : -1.53 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 190 HIS 0.002 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.017 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 *********************** 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: 35 poor density : 146 time to evaluate : 1.038 Fit side-chains REVERT: A 105 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 134 TRP cc_start: 0.8307 (OUTLIER) cc_final: 0.7728 (t60) REVERT: A 259 TYR cc_start: 0.8004 (m-80) cc_final: 0.7639 (m-80) REVERT: A 272 ARG cc_start: 0.7091 (ptp-170) cc_final: 0.4638 (mmt180) REVERT: A 317 ASN cc_start: 0.7821 (m-40) cc_final: 0.7526 (m-40) REVERT: A 325 TRP cc_start: 0.7515 (t60) cc_final: 0.6982 (t-100) REVERT: A 348 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.8069 (ptt90) REVERT: A 349 LEU cc_start: 0.8729 (tp) cc_final: 0.8362 (tt) REVERT: A 405 TRP cc_start: 0.8474 (m100) cc_final: 0.8241 (m100) REVERT: A 424 GLU cc_start: 0.8193 (tp30) cc_final: 0.7664 (tm-30) REVERT: B 190 TRP cc_start: 0.5782 (t-100) cc_final: 0.5239 (t60) REVERT: B 274 GLN cc_start: 0.8037 (mt0) cc_final: 0.7803 (mt0) REVERT: B 308 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 353 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8176 (pt) REVERT: B 528 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 588 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8594 (m) REVERT: C 89 ASP cc_start: 0.8044 (m-30) cc_final: 0.7078 (m-30) REVERT: C 176 GLN cc_start: 0.8264 (tt0) cc_final: 0.7249 (pp30) REVERT: C 201 ASN cc_start: 0.7264 (p0) cc_final: 0.6793 (p0) REVERT: C 214 LYS cc_start: 0.8070 (tttm) cc_final: 0.7728 (tttp) REVERT: D 17 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 129 GLU cc_start: 0.7464 (tt0) cc_final: 0.6903 (mp0) REVERT: D 151 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8092 (m-40) REVERT: D 185 LEU cc_start: 0.7697 (mt) cc_final: 0.7342 (mt) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.2078 time to fit residues: 49.9334 Evaluate side-chains 166 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 528 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.0050 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117357 restraints weight = 14750.574| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.32 r_work: 0.3261 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10190 Z= 0.206 Angle : 0.629 9.673 13918 Z= 0.295 Chirality : 0.041 0.157 1656 Planarity : 0.005 0.075 1711 Dihedral : 5.866 56.026 1787 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.36 % Allowed : 17.20 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1197 helix: -0.19 (0.24), residues: 461 sheet: -0.24 (0.39), residues: 184 loop : -1.50 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.002 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.014 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 ********************** 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 174 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.104 Fit side-chains REVERT: A 134 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7751 (t60) REVERT: A 259 TYR cc_start: 0.8209 (m-80) cc_final: 0.7837 (m-80) REVERT: A 272 ARG cc_start: 0.7159 (ptp-170) cc_final: 0.4890 (mmt180) REVERT: A 317 ASN cc_start: 0.7880 (m-40) cc_final: 0.7637 (m-40) REVERT: A 325 TRP cc_start: 0.7556 (t60) cc_final: 0.6968 (t-100) REVERT: A 348 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.8055 (ptt90) REVERT: A 349 LEU cc_start: 0.8715 (tp) cc_final: 0.8346 (tt) REVERT: A 424 GLU cc_start: 0.8268 (tp30) cc_final: 0.7688 (tm-30) REVERT: B 190 TRP cc_start: 0.5915 (t-100) cc_final: 0.5311 (t60) REVERT: B 274 GLN cc_start: 0.8324 (mt0) cc_final: 0.8006 (mt0) REVERT: B 308 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 353 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8270 (pt) REVERT: B 528 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: B 588 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 89 ASP cc_start: 0.8079 (m-30) cc_final: 0.6980 (m-30) REVERT: C 176 GLN cc_start: 0.8300 (tt0) cc_final: 0.7233 (pp30) REVERT: C 201 ASN cc_start: 0.7353 (p0) cc_final: 0.6912 (p0) REVERT: C 214 LYS cc_start: 0.8066 (tttm) cc_final: 0.7711 (tttp) REVERT: D 17 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8126 (mt-10) REVERT: D 129 GLU cc_start: 0.7485 (tt0) cc_final: 0.6887 (mp0) REVERT: D 151 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: D 185 LEU cc_start: 0.7755 (mt) cc_final: 0.7371 (mt) outliers start: 35 outliers final: 27 residues processed: 161 average time/residue: 0.2087 time to fit residues: 48.7931 Evaluate side-chains 167 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 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 528 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0030 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117925 restraints weight = 14675.678| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.31 r_work: 0.3271 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10190 Z= 0.192 Angle : 0.623 9.862 13918 Z= 0.292 Chirality : 0.041 0.154 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.722 53.000 1787 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 3.27 % Allowed : 17.77 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1197 helix: -0.13 (0.24), residues: 462 sheet: -0.21 (0.39), residues: 184 loop : -1.46 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 169 HIS 0.002 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.015 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5328.75 seconds wall clock time: 95 minutes 17.04 seconds (5717.04 seconds total)