Starting phenix.real_space_refine on Wed Sep 25 11:08:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_9849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_9849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_9849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_9849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/09_2024/6jmq_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-5461/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: 6.65, per 1000 atoms: 0.67 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: 2.47 Conformation dependent library (CDL) restraints added in 1.0 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: 1.18 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: 3.07 Time building geometry restraints manager: 2.88 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: 1.580 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: 0.100 Process input model: 25.340 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 111 SER cc_start: 0.7608 (m) cc_final: 0.7130 (p) REVERT: A 134 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7734 (t60) REVERT: A 259 TYR cc_start: 0.7910 (m-80) cc_final: 0.7371 (m-80) REVERT: A 272 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6789 (ptp-170) REVERT: A 325 TRP cc_start: 0.7324 (t60) cc_final: 0.7116 (t-100) REVERT: A 326 ILE cc_start: 0.8628 (tt) cc_final: 0.8369 (tt) REVERT: A 407 CYS cc_start: 0.7519 (m) cc_final: 0.7249 (m) REVERT: A 424 GLU cc_start: 0.7617 (tp30) cc_final: 0.6839 (tm-30) REVERT: B 325 THR cc_start: 0.9133 (p) cc_final: 0.8921 (t) REVERT: B 370 PHE cc_start: 0.8066 (t80) cc_final: 0.7462 (t80) REVERT: B 528 ASP cc_start: 0.8021 (t0) cc_final: 0.7815 (m-30) REVERT: B 607 SER cc_start: 0.8640 (p) cc_final: 0.8029 (m) REVERT: B 625 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7972 (mtm110) REVERT: C 89 ASP cc_start: 0.8085 (m-30) cc_final: 0.7014 (m-30) REVERT: D 6 GLN cc_start: 0.8495 (tt0) cc_final: 0.8218 (mt0) REVERT: D 42 TYR cc_start: 0.9058 (m-80) cc_final: 0.8823 (m-80) REVERT: D 156 ILE cc_start: 0.6044 (mt) cc_final: 0.5819 (mt) REVERT: D 176 ASP cc_start: 0.8609 (p0) cc_final: 0.7738 (p0) REVERT: D 201 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7460 (mm-30) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.2158 time to fit residues: 63.3561 Evaluate side-chains 143 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.138 Fit side-chains REVERT: A 54 ASN cc_start: 0.7182 (t160) cc_final: 0.6590 (m110) REVERT: A 134 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7758 (t60) REVERT: A 243 ILE cc_start: 0.7900 (tp) cc_final: 0.7628 (tp) REVERT: A 259 TYR cc_start: 0.7824 (m-80) cc_final: 0.7258 (m-80) REVERT: A 272 ARG cc_start: 0.7282 (ptp-170) cc_final: 0.4831 (mmt180) REVERT: A 325 TRP cc_start: 0.7329 (t60) cc_final: 0.7073 (t-100) REVERT: A 326 ILE cc_start: 0.8766 (tt) cc_final: 0.8515 (tt) REVERT: A 348 ARG cc_start: 0.8021 (ptm-80) cc_final: 0.7583 (ptt90) REVERT: A 349 LEU cc_start: 0.8798 (tp) cc_final: 0.8392 (tt) REVERT: A 424 GLU cc_start: 0.7760 (tp30) cc_final: 0.6885 (tm-30) REVERT: B 190 TRP cc_start: 0.4859 (t-100) cc_final: 0.3713 (t60) REVERT: B 231 GLN cc_start: 0.8064 (tp40) cc_final: 0.7852 (tp-100) REVERT: B 255 LYS cc_start: 0.8946 (mttm) cc_final: 0.8538 (mtmm) REVERT: C 89 ASP cc_start: 0.7911 (m-30) cc_final: 0.6889 (m-30) REVERT: C 212 ASP cc_start: 0.7870 (m-30) cc_final: 0.7664 (m-30) REVERT: C 214 LYS cc_start: 0.8176 (tttm) cc_final: 0.7618 (tttp) REVERT: D 156 ILE cc_start: 0.5607 (mt) cc_final: 0.5311 (mt) outliers start: 19 outliers final: 15 residues processed: 174 average time/residue: 0.2286 time to fit residues: 55.2644 Evaluate side-chains 156 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 82 optimal weight: 0.0040 overall best weight: 0.4606 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10190 Z= 0.186 Angle : 0.615 8.743 13918 Z= 0.300 Chirality : 0.041 0.220 1656 Planarity : 0.005 0.081 1711 Dihedral : 7.180 86.089 1787 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.59 % Allowed : 14.70 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1197 helix: -2.16 (0.21), residues: 454 sheet: -0.58 (0.38), residues: 175 loop : -2.00 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 190 HIS 0.002 0.001 HIS C 204 PHE 0.017 0.001 PHE A 336 TYR 0.013 0.001 TYR A 318 ARG 0.004 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 177 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.188 Fit side-chains REVERT: A 134 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7696 (t60) REVERT: A 272 ARG cc_start: 0.7345 (ptp-170) cc_final: 0.4756 (mmt180) REVERT: A 325 TRP cc_start: 0.7351 (t60) cc_final: 0.7040 (t-100) REVERT: A 326 ILE cc_start: 0.8737 (tt) cc_final: 0.8475 (tt) REVERT: A 348 ARG cc_start: 0.8059 (ptm-80) cc_final: 0.7593 (ptt90) REVERT: A 349 LEU cc_start: 0.8716 (tp) cc_final: 0.8250 (tt) REVERT: A 424 GLU cc_start: 0.7839 (tp30) cc_final: 0.7038 (tm-30) REVERT: B 190 TRP cc_start: 0.4620 (t-100) cc_final: 0.4071 (t60) REVERT: B 353 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7794 (pt) REVERT: B 528 ASP cc_start: 0.7863 (t0) cc_final: 0.7542 (m-30) REVERT: C 89 ASP cc_start: 0.7854 (m-30) cc_final: 0.6885 (m-30) REVERT: D 17 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7821 (mt-10) REVERT: D 129 GLU cc_start: 0.7399 (tt0) cc_final: 0.6867 (mp0) REVERT: D 156 ILE cc_start: 0.5628 (mt) cc_final: 0.5370 (mt) REVERT: D 185 LEU cc_start: 0.7033 (mt) cc_final: 0.6777 (mt) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 0.2284 time to fit residues: 54.3799 Evaluate side-chains 160 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain B residue 353 LEU 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 Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** B 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10190 Z= 0.273 Angle : 0.647 7.958 13918 Z= 0.315 Chirality : 0.043 0.232 1656 Planarity : 0.005 0.077 1711 Dihedral : 6.970 83.803 1787 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.94 % Allowed : 14.22 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1197 helix: -1.64 (0.22), residues: 455 sheet: -0.36 (0.38), residues: 180 loop : -1.86 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS D 204 PHE 0.015 0.001 PHE B 551 TYR 0.015 0.001 TYR B 453 ARG 0.004 0.001 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 188 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.070 Fit side-chains REVERT: A 134 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7626 (t60) REVERT: A 259 TYR cc_start: 0.7438 (m-80) cc_final: 0.7022 (m-80) REVERT: A 272 ARG cc_start: 0.7269 (ptp-170) cc_final: 0.4882 (mmt180) REVERT: A 325 TRP cc_start: 0.7516 (t60) cc_final: 0.7095 (t-100) REVERT: A 348 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7707 (ptt90) REVERT: A 349 LEU cc_start: 0.8757 (tp) cc_final: 0.8295 (tt) REVERT: A 424 GLU cc_start: 0.7801 (tp30) cc_final: 0.7130 (tm-30) REVERT: B 190 TRP cc_start: 0.4602 (t-100) cc_final: 0.4060 (t60) REVERT: B 353 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.7997 (pt) REVERT: B 528 ASP cc_start: 0.7996 (t0) cc_final: 0.7735 (m-30) REVERT: C 81 LYS cc_start: 0.8620 (tppt) cc_final: 0.8260 (mmtt) REVERT: C 89 ASP cc_start: 0.7981 (m-30) cc_final: 0.6885 (m-30) REVERT: C 176 GLN cc_start: 0.8130 (tt0) cc_final: 0.7113 (pp30) REVERT: D 129 GLU cc_start: 0.7554 (tt0) cc_final: 0.6954 (mp0) REVERT: D 151 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: D 156 ILE cc_start: 0.5627 (mt) cc_final: 0.5391 (mt) REVERT: D 185 LEU cc_start: 0.7284 (mt) cc_final: 0.6925 (mt) outliers start: 41 outliers final: 28 residues processed: 173 average time/residue: 0.1952 time to fit residues: 48.0617 Evaluate side-chains 169 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 221 THR Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain 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 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 98 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10190 Z= 0.182 Angle : 0.597 8.528 13918 Z= 0.287 Chirality : 0.041 0.212 1656 Planarity : 0.005 0.077 1711 Dihedral : 6.529 77.665 1787 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.07 % Allowed : 16.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.23), residues: 1197 helix: -1.17 (0.23), residues: 456 sheet: -0.48 (0.38), residues: 183 loop : -1.71 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 219 HIS 0.002 0.001 HIS C 204 PHE 0.015 0.001 PHE A 402 TYR 0.009 0.001 TYR D 146 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 185 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7597 (t60) REVERT: A 259 TYR cc_start: 0.7363 (m-80) cc_final: 0.7159 (m-80) REVERT: A 272 ARG cc_start: 0.7184 (ptp-170) cc_final: 0.4751 (mmt180) REVERT: A 317 ASN cc_start: 0.7919 (m-40) cc_final: 0.7556 (m-40) REVERT: A 325 TRP cc_start: 0.7385 (t60) cc_final: 0.6978 (t-100) REVERT: A 348 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7708 (ptt90) REVERT: A 349 LEU cc_start: 0.8644 (tp) cc_final: 0.8187 (tt) REVERT: A 424 GLU cc_start: 0.7826 (tp30) cc_final: 0.7318 (tm-30) REVERT: B 190 TRP cc_start: 0.4748 (t-100) cc_final: 0.4211 (t60) REVERT: B 308 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 353 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7951 (pt) REVERT: B 387 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7519 (tp40) REVERT: C 81 LYS cc_start: 0.8658 (tppt) cc_final: 0.8301 (mmtt) REVERT: C 89 ASP cc_start: 0.7825 (m-30) cc_final: 0.6854 (m-30) REVERT: C 176 GLN cc_start: 0.8047 (tt0) cc_final: 0.7061 (pp30) REVERT: D 17 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7761 (mt-10) REVERT: D 129 GLU cc_start: 0.7532 (tt0) cc_final: 0.6945 (mp0) REVERT: D 151 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: D 185 LEU cc_start: 0.7456 (mt) cc_final: 0.7146 (mt) outliers start: 32 outliers final: 25 residues processed: 177 average time/residue: 0.2106 time to fit residues: 53.0282 Evaluate side-chains 166 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 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 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10190 Z= 0.189 Angle : 0.600 10.473 13918 Z= 0.286 Chirality : 0.041 0.210 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.299 74.343 1787 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.94 % Allowed : 16.04 % 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: -1.75 (0.23), residues: 1197 helix: -0.83 (0.23), residues: 459 sheet: -0.42 (0.38), residues: 183 loop : -1.65 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS C 204 PHE 0.014 0.001 PHE A 336 TYR 0.015 0.001 TYR A 318 ARG 0.004 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 186 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7519 (t60) REVERT: A 259 TYR cc_start: 0.7604 (m-80) cc_final: 0.7254 (m-80) REVERT: A 272 ARG cc_start: 0.7144 (ptp-170) cc_final: 0.4697 (mmt180) REVERT: A 325 TRP cc_start: 0.7408 (t60) cc_final: 0.6954 (t-100) REVERT: A 348 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7682 (ptt90) REVERT: A 349 LEU cc_start: 0.8666 (tp) cc_final: 0.8212 (tt) REVERT: A 386 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 424 GLU cc_start: 0.7875 (tp30) cc_final: 0.7423 (tm-30) REVERT: B 190 TRP cc_start: 0.4798 (t-100) cc_final: 0.4381 (t60) REVERT: B 271 ASP cc_start: 0.7671 (t0) cc_final: 0.7357 (t0) REVERT: B 274 GLN cc_start: 0.7903 (mt0) cc_final: 0.7656 (mt0) REVERT: B 308 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 353 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7978 (pt) REVERT: B 387 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7511 (tp40) REVERT: B 528 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7276 (m-30) REVERT: C 81 LYS cc_start: 0.8630 (tppt) cc_final: 0.8221 (mmtt) REVERT: C 89 ASP cc_start: 0.7770 (m-30) cc_final: 0.6748 (m-30) REVERT: C 176 GLN cc_start: 0.8054 (tt0) cc_final: 0.7052 (pp30) REVERT: D 17 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7724 (mt-10) REVERT: D 129 GLU cc_start: 0.7609 (tt0) cc_final: 0.7023 (mp0) REVERT: D 151 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: D 185 LEU cc_start: 0.7597 (mt) cc_final: 0.7193 (mt) outliers start: 41 outliers final: 31 residues processed: 172 average time/residue: 0.2066 time to fit residues: 51.1343 Evaluate side-chains 178 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 0.0870 chunk 61 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2902 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= 0.200 Angle : 0.613 9.257 13918 Z= 0.293 Chirality : 0.041 0.198 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.105 69.744 1787 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.32 % Allowed : 15.75 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1197 helix: -0.58 (0.24), residues: 461 sheet: -0.34 (0.38), residues: 183 loop : -1.58 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.001 HIS C 204 PHE 0.013 0.001 PHE A 336 TYR 0.016 0.001 TYR A 318 ARG 0.006 0.000 ARG B 613 *********************** 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 188 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.7536 (t60) REVERT: A 259 TYR cc_start: 0.7641 (m-80) cc_final: 0.7281 (m-80) REVERT: A 272 ARG cc_start: 0.7146 (ptp-170) cc_final: 0.4699 (mmt180) REVERT: A 325 TRP cc_start: 0.7397 (t60) cc_final: 0.6893 (t-100) REVERT: A 348 ARG cc_start: 0.8130 (ptm-80) cc_final: 0.7695 (ptt90) REVERT: A 349 LEU cc_start: 0.8655 (tp) cc_final: 0.8257 (tt) REVERT: A 386 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 424 GLU cc_start: 0.7779 (tp30) cc_final: 0.7405 (tm-30) REVERT: B 190 TRP cc_start: 0.4881 (t-100) cc_final: 0.4443 (t60) REVERT: B 271 ASP cc_start: 0.7677 (t0) cc_final: 0.7399 (t0) REVERT: B 308 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 353 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 387 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7446 (tp40) REVERT: B 528 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: B 588 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8544 (m) REVERT: C 89 ASP cc_start: 0.7859 (m-30) cc_final: 0.6822 (m-30) REVERT: C 176 GLN cc_start: 0.8097 (tt0) cc_final: 0.7109 (pp30) REVERT: C 201 ASN cc_start: 0.7351 (p0) cc_final: 0.6927 (p0) REVERT: D 17 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 129 GLU cc_start: 0.7539 (tt0) cc_final: 0.6964 (mp0) REVERT: D 151 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7748 (m-40) REVERT: D 185 LEU cc_start: 0.7639 (mt) cc_final: 0.7217 (mt) outliers start: 45 outliers final: 32 residues processed: 175 average time/residue: 0.2011 time to fit residues: 50.5412 Evaluate side-chains 174 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10190 Z= 0.293 Angle : 0.662 9.052 13918 Z= 0.318 Chirality : 0.043 0.199 1656 Planarity : 0.005 0.076 1711 Dihedral : 6.226 67.143 1787 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.03 % Allowed : 16.14 % Favored : 79.83 % 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: -1.54 (0.23), residues: 1197 helix: -0.55 (0.24), residues: 456 sheet: -0.37 (0.37), residues: 191 loop : -1.61 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.004 0.001 HIS C 204 PHE 0.014 0.001 PHE C 151 TYR 0.016 0.002 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 182 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 140 time to evaluate : 1.087 Fit side-chains REVERT: A 134 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7620 (t60) REVERT: A 259 TYR cc_start: 0.7710 (m-80) cc_final: 0.7349 (m-80) REVERT: A 272 ARG cc_start: 0.7234 (ptp-170) cc_final: 0.4800 (mmt180) REVERT: A 325 TRP cc_start: 0.7499 (t60) cc_final: 0.6967 (t-100) REVERT: A 348 ARG cc_start: 0.8126 (ptm-80) cc_final: 0.7680 (ptt90) REVERT: A 349 LEU cc_start: 0.8738 (tp) cc_final: 0.8303 (tt) REVERT: A 386 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 424 GLU cc_start: 0.7778 (tp30) cc_final: 0.7406 (tm-30) REVERT: B 190 TRP cc_start: 0.5300 (t-100) cc_final: 0.4650 (t60) REVERT: B 308 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8509 (mm) REVERT: B 353 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8069 (pt) REVERT: B 387 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7557 (tp40) REVERT: B 528 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: C 89 ASP cc_start: 0.7906 (m-30) cc_final: 0.6581 (m-30) REVERT: C 176 GLN cc_start: 0.8090 (tt0) cc_final: 0.7041 (pp30) REVERT: C 201 ASN cc_start: 0.7481 (p0) cc_final: 0.7091 (p0) REVERT: D 17 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 129 GLU cc_start: 0.7546 (tt0) cc_final: 0.6938 (mp0) REVERT: D 151 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: D 185 LEU cc_start: 0.7657 (mt) cc_final: 0.7217 (mt) outliers start: 42 outliers final: 31 residues processed: 167 average time/residue: 0.1998 time to fit residues: 47.9665 Evaluate side-chains 171 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 386 LEU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 395 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 61 optimal weight: 0.0010 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.0270 chunk 65 optimal weight: 0.5980 overall best weight: 0.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3125 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= 0.149 Angle : 0.595 9.968 13918 Z= 0.282 Chirality : 0.040 0.162 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.984 58.392 1787 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 17.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1197 helix: -0.22 (0.24), residues: 459 sheet: -0.33 (0.38), residues: 185 loop : -1.52 (0.25), residues: 553 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 0.013 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 179 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 134 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7509 (t60) REVERT: A 259 TYR cc_start: 0.7731 (m-80) cc_final: 0.7399 (m-80) REVERT: A 272 ARG cc_start: 0.7145 (ptp-170) cc_final: 0.4664 (mmt180) REVERT: A 325 TRP cc_start: 0.7413 (t60) cc_final: 0.6836 (t-100) REVERT: A 348 ARG cc_start: 0.8151 (ptm-80) cc_final: 0.7731 (ptt90) REVERT: A 349 LEU cc_start: 0.8630 (tp) cc_final: 0.8255 (tt) REVERT: A 424 GLU cc_start: 0.7760 (tp30) cc_final: 0.7468 (tm-30) REVERT: B 190 TRP cc_start: 0.5348 (t-100) cc_final: 0.4939 (t60) REVERT: B 308 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 353 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7976 (pt) REVERT: B 528 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: B 588 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (m) REVERT: C 89 ASP cc_start: 0.7708 (m-30) cc_final: 0.6906 (m-30) REVERT: C 176 GLN cc_start: 0.8104 (tt0) cc_final: 0.7105 (pp30) REVERT: C 201 ASN cc_start: 0.7232 (p0) cc_final: 0.6875 (p0) REVERT: D 17 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 129 GLU cc_start: 0.7538 (tt0) cc_final: 0.6937 (mp0) REVERT: D 151 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: D 185 LEU cc_start: 0.7614 (mt) cc_final: 0.7195 (mt) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.2067 time to fit residues: 48.8359 Evaluate side-chains 162 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 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 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 95 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 overall best weight: 0.4414 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10190 Z= 0.184 Angle : 0.620 9.838 13918 Z= 0.295 Chirality : 0.041 0.153 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.860 59.649 1787 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.98 % Allowed : 17.87 % 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: -1.22 (0.24), residues: 1197 helix: -0.16 (0.24), residues: 462 sheet: -0.24 (0.39), residues: 183 loop : -1.54 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS A 420 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 166 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7587 (t60) REVERT: A 259 TYR cc_start: 0.7780 (m-80) cc_final: 0.7439 (m-80) REVERT: A 272 ARG cc_start: 0.7250 (ptp-170) cc_final: 0.4947 (mmt180) REVERT: A 325 TRP cc_start: 0.7388 (t60) cc_final: 0.6783 (t-100) REVERT: A 348 ARG cc_start: 0.8144 (ptm-80) cc_final: 0.7681 (ptt90) REVERT: A 349 LEU cc_start: 0.8636 (tp) cc_final: 0.8270 (tt) REVERT: A 424 GLU cc_start: 0.7830 (tp30) cc_final: 0.7549 (tm-30) REVERT: B 190 TRP cc_start: 0.5367 (t-100) cc_final: 0.4949 (t60) REVERT: B 308 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 353 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8010 (pt) REVERT: B 528 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: C 89 ASP cc_start: 0.7809 (m-30) cc_final: 0.6908 (m-30) REVERT: C 176 GLN cc_start: 0.8107 (tt0) cc_final: 0.7092 (pp30) REVERT: C 201 ASN cc_start: 0.7167 (p0) cc_final: 0.6908 (p0) REVERT: D 17 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7669 (mt-10) REVERT: D 129 GLU cc_start: 0.7545 (tt0) cc_final: 0.6936 (mp0) REVERT: D 151 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: D 185 LEU cc_start: 0.7653 (mt) cc_final: 0.7232 (mt) outliers start: 31 outliers final: 24 residues processed: 154 average time/residue: 0.2160 time to fit residues: 47.6078 Evaluate side-chains 159 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 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 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 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 82 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126293 restraints weight = 14622.259| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.39 r_work: 0.3184 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10190 Z= 0.205 Angle : 0.630 9.618 13918 Z= 0.300 Chirality : 0.041 0.152 1656 Planarity : 0.005 0.076 1711 Dihedral : 5.785 57.357 1787 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 3.27 % Allowed : 17.58 % 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: -1.20 (0.24), residues: 1197 helix: -0.12 (0.24), residues: 462 sheet: -0.28 (0.39), residues: 184 loop : -1.52 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 405 HIS 0.003 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.07 seconds wall clock time: 41 minutes 43.97 seconds (2503.97 seconds total)