Starting phenix.real_space_refine on Fri Jun 13 07:11:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.map" model { file = "/net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zny_14842/06_2025/7zny_14842.cif" } resolution = 3.26 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= 0.018 sd= 0.131 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 84 5.16 5 C 9442 2.51 5 N 2440 2.21 5 O 2797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14763 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3722 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 29, 'TRANS': 443} Chain: "B" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3683 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 29, 'TRANS': 439} Chain: "C" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3664 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 29, 'TRANS': 437} Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3694 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 29, 'TRANS': 440} Time building chain proxies: 9.88, per 1000 atoms: 0.67 Number of scatterers: 14763 At special positions: 0 Unit cell: (117.546, 124.004, 161.464, 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 84 16.00 O 2797 8.00 N 2440 7.00 C 9442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 602 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 390 " distance=2.20 Simple disulfide: pdb=" SG CYS B 566 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS D 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS D 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 602 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 602 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 377 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 566 " - pdb=" SG CYS D 575 " 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 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.9 seconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 36 sheets defined 13.6% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.674A pdb=" N ASN A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 180 Proline residue: A 169 - end of helix removed outlier: 4.356A pdb=" N GLY A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.975A pdb=" N ASP A 309 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 removed outlier: 4.291A pdb=" N ASN A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.897A pdb=" N CYS A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 180 Proline residue: B 169 - end of helix removed outlier: 3.638A pdb=" N GLY B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.043A pdb=" N GLU B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 4.051A pdb=" N CYS B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 179 Proline residue: C 169 - end of helix removed outlier: 4.592A pdb=" N GLY C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.618A pdb=" N ARG C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 removed outlier: 4.368A pdb=" N ASP C 309 " --> pdb=" O HIS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 383 removed outlier: 3.667A pdb=" N GLN C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 4.227A pdb=" N CYS C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.673A pdb=" N TYR D 153 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 180 Proline residue: D 169 - end of helix removed outlier: 3.572A pdb=" N ALA D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.844A pdb=" N ALA D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS D 281 " --> pdb=" O SER D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 281' Processing helix chain 'D' and resid 371 through 383 removed outlier: 3.943A pdb=" N GLN D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 392 removed outlier: 3.871A pdb=" N CYS D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 removed outlier: 3.756A pdb=" N TRP A 138 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 138 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C 137 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 198 removed outlier: 3.540A pdb=" N VAL A 592 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 582 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.698A pdb=" N TYR A 228 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 270 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 255 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A 268 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS A 257 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 266 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 303 removed outlier: 4.195A pdb=" N LYS A 344 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 353 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 303 removed outlier: 4.195A pdb=" N LYS A 344 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 422 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AB1, first strand: chain 'A' and resid 447 through 448 removed outlier: 7.841A pdb=" N ILE A 463 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS A 477 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 506 through 507 removed outlier: 4.284A pdb=" N TYR A 520 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 522 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 193 through 199 removed outlier: 4.390A pdb=" N THR B 193 " --> pdb=" O SER B 601 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 601 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 595 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 594 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 577 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 221 removed outlier: 4.787A pdb=" N ASN B 218 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 233 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB6, first strand: chain 'B' and resid 302 through 303 removed outlier: 4.423A pdb=" N LYS B 344 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 366 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 362 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG B 351 " --> pdb=" O MET B 362 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 350 through 355 current: chain 'B' and resid 422 through 426 Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 321 removed outlier: 6.528A pdb=" N ILE B 285 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 354 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 287 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG B 351 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 362 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AB9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.586A pdb=" N LEU B 462 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 463 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 511 through 512 removed outlier: 3.772A pdb=" N ILE B 534 " --> pdb=" O TYR B 549 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 193 through 199 removed outlier: 3.874A pdb=" N LEU C 595 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 573 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C 561 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 215 through 224 removed outlier: 6.238A pdb=" N ILE C 216 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL C 235 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN C 218 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C 233 " --> pdb=" O ASN C 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 255 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR C 268 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS C 257 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 266 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.571A pdb=" N GLU C 333 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.901A pdb=" N LYS C 344 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 366 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 353 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.901A pdb=" N LYS C 344 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 366 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 406 " --> pdb=" O THR C 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 350 through 351 removed outlier: 4.125A pdb=" N ARG C 351 " --> pdb=" O MET C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 440 through 441 Processing sheet with id=AC9, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AD1, first strand: chain 'D' and resid 193 through 199 removed outlier: 3.706A pdb=" N THR D 193 " --> pdb=" O SER D 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 601 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 595 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 581 " --> pdb=" O THR D 590 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP D 574 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS D 566 " --> pdb=" O TRP D 574 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS D 576 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE D 564 " --> pdb=" O HIS D 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE D 578 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 562 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG D 580 " --> pdb=" O ASP D 560 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 215 through 221 removed outlier: 3.921A pdb=" N GLU D 215 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET D 219 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR D 231 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 221 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY D 229 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 215 through 221 removed outlier: 3.921A pdb=" N GLU D 215 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET D 219 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR D 231 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 221 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY D 229 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 330 through 333 removed outlier: 6.909A pdb=" N ILE D 285 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE D 354 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL D 287 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 353 " --> pdb=" O THR D 360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 301 through 303 removed outlier: 3.736A pdb=" N LYS D 344 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 438 through 441 Processing sheet with id=AD7, first strand: chain 'D' and resid 438 through 441 Processing sheet with id=AD8, first strand: chain 'D' and resid 480 through 481 Processing sheet with id=AD9, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.561A pdb=" N TYR D 520 " --> pdb=" O TYR D 539 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 534 " --> pdb=" O TYR D 549 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3638 1.33 - 1.45: 2963 1.45 - 1.57: 8405 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 15126 Sorted by residual: bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.461 1.497 -0.036 9.10e-03 1.21e+04 1.60e+01 bond pdb=" N THR A 480 " pdb=" CA THR A 480 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N GLY B 314 " pdb=" CA GLY B 314 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.02e-02 9.61e+03 1.11e+01 bond pdb=" N THR C 326 " pdb=" CA THR C 326 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.11e+01 bond pdb=" N ILE C 335 " pdb=" CA ILE C 335 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.10e-03 1.21e+04 1.04e+01 ... (remaining 15121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 20170 1.95 - 3.90: 401 3.90 - 5.86: 35 5.86 - 7.81: 8 7.81 - 9.76: 4 Bond angle restraints: 20618 Sorted by residual: angle pdb=" C TYR D 491 " pdb=" CA TYR D 491 " pdb=" CB TYR D 491 " ideal model delta sigma weight residual 109.38 116.54 -7.16 1.80e+00 3.09e-01 1.58e+01 angle pdb=" CA GLY B 399 " pdb=" C GLY B 399 " pdb=" O GLY B 399 " ideal model delta sigma weight residual 121.41 118.01 3.40 8.80e-01 1.29e+00 1.50e+01 angle pdb=" N PRO D 185 " pdb=" CA PRO D 185 " pdb=" C PRO D 185 " ideal model delta sigma weight residual 113.53 118.82 -5.29 1.39e+00 5.18e-01 1.45e+01 angle pdb=" CB GLU B 333 " pdb=" CG GLU B 333 " pdb=" CD GLU B 333 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" C ASP A 570 " pdb=" N ASP A 571 " pdb=" CA ASP A 571 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 ... (remaining 20613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8273 17.95 - 35.89: 700 35.89 - 53.83: 106 53.83 - 71.78: 19 71.78 - 89.72: 3 Dihedral angle restraints: 9101 sinusoidal: 3632 harmonic: 5469 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 602 " pdb=" CB CYS B 602 " ideal model delta sinusoidal sigma weight residual -86.00 -144.82 58.82 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 9098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1930 0.060 - 0.120: 369 0.120 - 0.180: 43 0.180 - 0.240: 8 0.240 - 0.300: 1 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CA LEU A 479 " pdb=" N LEU A 479 " pdb=" C LEU A 479 " pdb=" CB LEU A 479 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA VAL D 367 " pdb=" N VAL D 367 " pdb=" C VAL D 367 " pdb=" CB VAL D 367 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR C 326 " pdb=" N THR C 326 " pdb=" C THR C 326 " pdb=" CB THR C 326 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2348 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 490 " 0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C CYS D 490 " -0.092 2.00e-02 2.50e+03 pdb=" O CYS D 490 " 0.034 2.00e-02 2.50e+03 pdb=" N TYR D 491 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 185 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C PRO D 185 " -0.068 2.00e-02 2.50e+03 pdb=" O PRO D 185 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR D 186 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 313 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP B 313 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP B 313 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY B 314 " 0.020 2.00e-02 2.50e+03 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2307 2.77 - 3.30: 13682 3.30 - 3.83: 23264 3.83 - 4.37: 26548 4.37 - 4.90: 48046 Nonbonded interactions: 113847 Sorted by model distance: nonbonded pdb=" OH TYR C 536 " pdb=" OE1 GLN C 577 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 228 " pdb=" OE2 GLU A 252 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 406 " pdb=" OD1 ASN A 464 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 348 " pdb=" O ASP C 435 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" OE2 GLU B 252 " model vdw 2.277 3.040 ... (remaining 113842 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 136 through 602) selection = (chain 'B' and resid 136 through 602) selection = chain 'C' selection = (chain 'D' and resid 136 through 602) } 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: 0.880 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.630 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.004 0.170 15150 Z= 0.225 Angle : 0.636 9.762 20666 Z= 0.364 Chirality : 0.049 0.300 2351 Planarity : 0.005 0.053 2638 Dihedral : 12.596 89.724 5519 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.12 (0.19), residues: 1871 helix: 1.65 (0.37), residues: 234 sheet: -0.31 (0.21), residues: 667 loop : -1.70 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 138 HIS 0.005 0.001 HIS B 532 PHE 0.021 0.001 PHE B 398 TYR 0.016 0.001 TYR D 439 ARG 0.004 0.000 ARG D 552 Details of bonding type rmsd hydrogen bonds : bond 0.21266 ( 463) hydrogen bonds : angle 8.84798 ( 1305) SS BOND : bond 0.03472 ( 24) SS BOND : angle 1.28920 ( 48) covalent geometry : bond 0.00347 (15126) covalent geometry : angle 0.63358 (20618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.2654 (mtt) cc_final: 0.0890 (tmm) REVERT: B 316 LEU cc_start: 0.7793 (tp) cc_final: 0.7461 (mt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2707 time to fit residues: 51.4803 Evaluate side-chains 100 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.198581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166282 restraints weight = 17251.179| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.56 r_work: 0.3714 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15150 Z= 0.138 Angle : 0.587 11.816 20666 Z= 0.300 Chirality : 0.048 0.193 2351 Planarity : 0.004 0.047 2638 Dihedral : 4.428 23.828 2046 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.33 % Allowed : 14.87 % Favored : 82.81 % 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: -1.06 (0.19), residues: 1871 helix: 1.71 (0.37), residues: 231 sheet: -0.37 (0.20), residues: 694 loop : -1.60 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 138 HIS 0.004 0.001 HIS B 477 PHE 0.017 0.001 PHE B 353 TYR 0.020 0.001 TYR A 520 ARG 0.003 0.000 ARG D 552 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 463) hydrogen bonds : angle 6.27697 ( 1305) SS BOND : bond 0.00410 ( 24) SS BOND : angle 1.36336 ( 48) covalent geometry : bond 0.00318 (15126) covalent geometry : angle 0.58405 (20618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.2746 (mtt) cc_final: 0.1821 (ttm) REVERT: B 491 TYR cc_start: 0.6186 (m-80) cc_final: 0.5914 (m-80) REVERT: C 331 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7803 (m) outliers start: 39 outliers final: 16 residues processed: 135 average time/residue: 0.2277 time to fit residues: 49.1558 Evaluate side-chains 116 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 139 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.190121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139774 restraints weight = 17617.979| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.14 r_work: 0.3567 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15150 Z= 0.237 Angle : 0.665 11.522 20666 Z= 0.338 Chirality : 0.050 0.187 2351 Planarity : 0.005 0.047 2638 Dihedral : 4.894 23.980 2046 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.88 % Allowed : 13.91 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.19), residues: 1871 helix: 1.56 (0.36), residues: 231 sheet: -0.49 (0.20), residues: 694 loop : -1.72 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 138 HIS 0.005 0.001 HIS D 576 PHE 0.022 0.002 PHE B 323 TYR 0.016 0.002 TYR B 547 ARG 0.008 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 463) hydrogen bonds : angle 5.94516 ( 1305) SS BOND : bond 0.00463 ( 24) SS BOND : angle 1.52845 ( 48) covalent geometry : bond 0.00563 (15126) covalent geometry : angle 0.66126 (20618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 112 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 339 HIS cc_start: 0.5451 (OUTLIER) cc_final: 0.4338 (m90) REVERT: A 500 MET cc_start: 0.2998 (mtt) cc_final: 0.2012 (ttm) REVERT: B 491 TYR cc_start: 0.5989 (m-80) cc_final: 0.5628 (m-80) REVERT: C 303 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8543 (tp) outliers start: 65 outliers final: 41 residues processed: 165 average time/residue: 0.2395 time to fit residues: 64.4377 Evaluate side-chains 144 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 568 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN B 517 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140573 restraints weight = 17531.295| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.05 r_work: 0.3628 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15150 Z= 0.124 Angle : 0.578 10.708 20666 Z= 0.294 Chirality : 0.047 0.181 2351 Planarity : 0.004 0.062 2638 Dihedral : 4.544 20.359 2046 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.75 % Allowed : 16.00 % Favored : 81.25 % 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: -1.12 (0.19), residues: 1871 helix: 1.69 (0.36), residues: 232 sheet: -0.42 (0.20), residues: 692 loop : -1.64 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 259 HIS 0.003 0.001 HIS D 350 PHE 0.013 0.001 PHE B 353 TYR 0.015 0.001 TYR A 520 ARG 0.003 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 463) hydrogen bonds : angle 5.49482 ( 1305) SS BOND : bond 0.00221 ( 24) SS BOND : angle 1.45990 ( 48) covalent geometry : bond 0.00286 (15126) covalent geometry : angle 0.57457 (20618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 339 HIS cc_start: 0.5403 (OUTLIER) cc_final: 0.4117 (m90) REVERT: A 500 MET cc_start: 0.3151 (mtt) cc_final: 0.2462 (ttm) REVERT: B 153 TYR cc_start: 0.7871 (m-10) cc_final: 0.7521 (m-80) REVERT: B 491 TYR cc_start: 0.6086 (m-80) cc_final: 0.5724 (m-80) REVERT: C 207 MET cc_start: 0.8469 (mtp) cc_final: 0.8225 (mtm) REVERT: C 303 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8600 (tp) REVERT: C 331 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7706 (m) REVERT: C 535 VAL cc_start: 0.8240 (t) cc_final: 0.7964 (t) REVERT: D 261 ASN cc_start: 0.8424 (t0) cc_final: 0.7956 (t0) outliers start: 46 outliers final: 29 residues processed: 143 average time/residue: 0.2279 time to fit residues: 52.2154 Evaluate side-chains 135 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN D 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.189173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138854 restraints weight = 17801.257| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.25 r_work: 0.3553 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15150 Z= 0.230 Angle : 0.663 11.091 20666 Z= 0.335 Chirality : 0.050 0.193 2351 Planarity : 0.005 0.061 2638 Dihedral : 4.924 21.124 2046 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.24 % Allowed : 15.58 % Favored : 80.18 % 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: -1.26 (0.19), residues: 1871 helix: 1.63 (0.37), residues: 225 sheet: -0.58 (0.20), residues: 698 loop : -1.67 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 138 HIS 0.006 0.001 HIS D 576 PHE 0.019 0.002 PHE B 353 TYR 0.013 0.002 TYR B 520 ARG 0.007 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 463) hydrogen bonds : angle 5.60726 ( 1305) SS BOND : bond 0.00349 ( 24) SS BOND : angle 1.62834 ( 48) covalent geometry : bond 0.00547 (15126) covalent geometry : angle 0.65884 (20618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 114 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 HIS cc_start: 0.5489 (OUTLIER) cc_final: 0.4114 (m90) REVERT: A 500 MET cc_start: 0.3117 (mtt) cc_final: 0.2077 (ttm) REVERT: B 153 TYR cc_start: 0.7998 (m-10) cc_final: 0.7572 (m-80) REVERT: B 257 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (mttm) REVERT: B 491 TYR cc_start: 0.6106 (m-80) cc_final: 0.5750 (m-80) REVERT: C 217 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8451 (pt) REVERT: C 303 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 261 ASN cc_start: 0.8445 (t0) cc_final: 0.7943 (t0) outliers start: 71 outliers final: 52 residues processed: 171 average time/residue: 0.2431 time to fit residues: 67.9204 Evaluate side-chains 161 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 568 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 HIS ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142678 restraints weight = 17634.318| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.23 r_work: 0.3608 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15150 Z= 0.116 Angle : 0.572 10.349 20666 Z= 0.289 Chirality : 0.047 0.206 2351 Planarity : 0.004 0.058 2638 Dihedral : 4.500 19.282 2046 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.16 % Allowed : 17.61 % Favored : 79.22 % 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: -1.17 (0.19), residues: 1871 helix: 1.75 (0.37), residues: 225 sheet: -0.44 (0.20), residues: 688 loop : -1.69 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 259 HIS 0.004 0.001 HIS D 532 PHE 0.013 0.001 PHE B 353 TYR 0.014 0.001 TYR A 520 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 463) hydrogen bonds : angle 5.20894 ( 1305) SS BOND : bond 0.00196 ( 24) SS BOND : angle 1.26636 ( 48) covalent geometry : bond 0.00268 (15126) covalent geometry : angle 0.56973 (20618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.3146 (mtt) cc_final: 0.2171 (ttm) REVERT: B 153 TYR cc_start: 0.7833 (m-10) cc_final: 0.7554 (m-80) REVERT: B 257 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (mttm) REVERT: B 479 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 491 TYR cc_start: 0.5954 (m-80) cc_final: 0.5641 (m-80) REVERT: C 207 MET cc_start: 0.8581 (mtp) cc_final: 0.8284 (mtm) REVERT: C 217 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8350 (pt) REVERT: C 303 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8594 (tp) REVERT: C 331 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7748 (m) REVERT: D 261 ASN cc_start: 0.8394 (t0) cc_final: 0.7909 (t0) outliers start: 53 outliers final: 38 residues processed: 146 average time/residue: 0.2282 time to fit residues: 54.8932 Evaluate side-chains 141 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 119 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.193474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141618 restraints weight = 17676.312| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.04 r_work: 0.3642 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15150 Z= 0.114 Angle : 0.565 10.166 20666 Z= 0.285 Chirality : 0.047 0.251 2351 Planarity : 0.004 0.058 2638 Dihedral : 4.402 20.244 2046 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.28 % Allowed : 17.85 % Favored : 78.87 % 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: -1.08 (0.19), residues: 1871 helix: 1.80 (0.37), residues: 226 sheet: -0.34 (0.20), residues: 682 loop : -1.64 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 138 HIS 0.008 0.001 HIS D 350 PHE 0.018 0.001 PHE B 251 TYR 0.014 0.001 TYR A 520 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.02795 ( 463) hydrogen bonds : angle 5.08968 ( 1305) SS BOND : bond 0.00213 ( 24) SS BOND : angle 1.50051 ( 48) covalent geometry : bond 0.00263 (15126) covalent geometry : angle 0.56095 (20618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.3086 (mtt) cc_final: 0.2140 (ttm) REVERT: B 153 TYR cc_start: 0.7853 (m-10) cc_final: 0.7535 (m-80) REVERT: B 257 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8179 (mttm) REVERT: B 471 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7389 (pp30) REVERT: B 479 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7377 (tp) REVERT: B 491 TYR cc_start: 0.5956 (m-80) cc_final: 0.5643 (m-80) REVERT: C 207 MET cc_start: 0.8568 (mtp) cc_final: 0.8251 (mtm) REVERT: C 217 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8345 (pt) REVERT: C 331 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7757 (m) REVERT: D 261 ASN cc_start: 0.8349 (t0) cc_final: 0.7878 (t0) outliers start: 55 outliers final: 43 residues processed: 154 average time/residue: 0.2668 time to fit residues: 68.9324 Evaluate side-chains 148 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 HIS C 517 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.191814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142977 restraints weight = 17689.300| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.16 r_work: 0.3584 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15150 Z= 0.158 Angle : 0.591 10.022 20666 Z= 0.298 Chirality : 0.048 0.235 2351 Planarity : 0.004 0.060 2638 Dihedral : 4.487 20.090 2046 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.52 % Allowed : 17.67 % Favored : 78.81 % 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: -1.12 (0.19), residues: 1871 helix: 1.80 (0.37), residues: 226 sheet: -0.39 (0.20), residues: 688 loop : -1.66 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 138 HIS 0.003 0.001 HIS D 576 PHE 0.014 0.001 PHE B 353 TYR 0.013 0.001 TYR B 520 ARG 0.004 0.000 ARG C 563 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 463) hydrogen bonds : angle 5.13174 ( 1305) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.43936 ( 48) covalent geometry : bond 0.00376 (15126) covalent geometry : angle 0.58810 (20618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 103 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 328 MET cc_start: 0.7868 (mpp) cc_final: 0.7281 (mtt) REVERT: A 500 MET cc_start: 0.3159 (mtt) cc_final: 0.2136 (ttm) REVERT: B 153 TYR cc_start: 0.7897 (m-10) cc_final: 0.7632 (m-80) REVERT: B 257 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8265 (mttm) REVERT: B 479 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7422 (tp) REVERT: B 491 TYR cc_start: 0.5969 (m-80) cc_final: 0.5633 (m-80) REVERT: C 217 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (pt) REVERT: C 303 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8594 (tp) REVERT: C 331 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7803 (m) REVERT: D 261 ASN cc_start: 0.8391 (t0) cc_final: 0.7927 (t0) outliers start: 59 outliers final: 50 residues processed: 154 average time/residue: 0.2712 time to fit residues: 68.3154 Evaluate side-chains 156 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 101 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139350 restraints weight = 17732.396| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.05 r_work: 0.3561 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15150 Z= 0.243 Angle : 0.667 11.700 20666 Z= 0.337 Chirality : 0.050 0.248 2351 Planarity : 0.005 0.062 2638 Dihedral : 4.829 21.413 2046 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.88 % Allowed : 17.37 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1871 helix: 1.81 (0.37), residues: 219 sheet: -0.57 (0.20), residues: 677 loop : -1.72 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 138 HIS 0.014 0.001 HIS D 350 PHE 0.019 0.002 PHE B 353 TYR 0.013 0.002 TYR B 520 ARG 0.008 0.000 ARG D 351 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 463) hydrogen bonds : angle 5.39277 ( 1305) SS BOND : bond 0.00361 ( 24) SS BOND : angle 1.58906 ( 48) covalent geometry : bond 0.00582 (15126) covalent geometry : angle 0.66286 (20618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 106 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7590 (mtm-85) REVERT: A 328 MET cc_start: 0.7705 (mpp) cc_final: 0.7270 (mtm) REVERT: A 500 MET cc_start: 0.3175 (mtt) cc_final: 0.2086 (ttm) REVERT: B 153 TYR cc_start: 0.7986 (m-10) cc_final: 0.7624 (m-80) REVERT: B 257 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (mttm) REVERT: B 479 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7404 (tp) REVERT: B 491 TYR cc_start: 0.6106 (m-80) cc_final: 0.5830 (m-80) REVERT: C 217 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8456 (pt) REVERT: C 303 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8612 (tp) REVERT: D 261 ASN cc_start: 0.8339 (t0) cc_final: 0.7835 (t0) outliers start: 65 outliers final: 56 residues processed: 160 average time/residue: 0.2397 time to fit residues: 63.0472 Evaluate side-chains 160 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 100 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 149 optimal weight: 0.0970 chunk 148 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.193571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145589 restraints weight = 17616.468| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.11 r_work: 0.3619 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15150 Z= 0.107 Angle : 0.574 10.049 20666 Z= 0.288 Chirality : 0.047 0.252 2351 Planarity : 0.004 0.062 2638 Dihedral : 4.431 19.921 2046 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.16 % Allowed : 18.03 % Favored : 78.81 % 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: -1.10 (0.19), residues: 1871 helix: 1.97 (0.37), residues: 221 sheet: -0.38 (0.20), residues: 677 loop : -1.67 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 138 HIS 0.004 0.001 HIS B 477 PHE 0.013 0.001 PHE B 251 TYR 0.014 0.001 TYR A 520 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.02735 ( 463) hydrogen bonds : angle 5.05016 ( 1305) SS BOND : bond 0.00190 ( 24) SS BOND : angle 1.26330 ( 48) covalent geometry : bond 0.00244 (15126) covalent geometry : angle 0.57125 (20618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 2.915 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7592 (mtm-85) REVERT: A 328 MET cc_start: 0.7567 (mpp) cc_final: 0.7285 (mtm) REVERT: A 500 MET cc_start: 0.3089 (mtt) cc_final: 0.2071 (ttm) REVERT: B 153 TYR cc_start: 0.7879 (m-10) cc_final: 0.7550 (m-80) REVERT: B 257 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8225 (mttm) REVERT: B 479 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7425 (tp) REVERT: B 491 TYR cc_start: 0.5971 (m-80) cc_final: 0.5649 (m-80) REVERT: C 217 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (pt) REVERT: C 303 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8614 (tp) REVERT: C 331 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7804 (m) REVERT: C 535 VAL cc_start: 0.8066 (t) cc_final: 0.7762 (t) REVERT: D 261 ASN cc_start: 0.8307 (t0) cc_final: 0.7829 (t0) outliers start: 53 outliers final: 43 residues processed: 148 average time/residue: 0.2723 time to fit residues: 66.3509 Evaluate side-chains 150 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.191850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142972 restraints weight = 17680.912| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.15 r_work: 0.3602 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15150 Z= 0.152 Angle : 0.594 10.280 20666 Z= 0.299 Chirality : 0.048 0.256 2351 Planarity : 0.004 0.061 2638 Dihedral : 4.480 19.637 2046 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.22 % Allowed : 17.85 % Favored : 78.93 % 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: -1.13 (0.19), residues: 1871 helix: 1.93 (0.37), residues: 221 sheet: -0.40 (0.20), residues: 677 loop : -1.68 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 138 HIS 0.004 0.001 HIS D 339 PHE 0.015 0.001 PHE B 353 TYR 0.013 0.001 TYR B 520 ARG 0.003 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 463) hydrogen bonds : angle 5.07397 ( 1305) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.40842 ( 48) covalent geometry : bond 0.00360 (15126) covalent geometry : angle 0.59063 (20618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8245.46 seconds wall clock time: 148 minutes 12.52 seconds (8892.52 seconds total)