Starting phenix.real_space_refine on Sun Aug 24 09:30:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.map" model { file = "/net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ur8_42487/08_2025/8ur8_42487.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 88 5.16 5 C 11964 2.51 5 N 3088 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N ARG A 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG A 78 " occ=0.86 residue: pdb=" N GLY A 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY A 79 " occ=0.82 residue: pdb=" N GLY A 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY A 80 " occ=0.83 residue: pdb=" N ARG A 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG A 81 " occ=0.62 residue: pdb=" N ARG B 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG B 78 " occ=0.86 residue: pdb=" N GLY B 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY B 79 " occ=0.82 residue: pdb=" N GLY B 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY B 80 " occ=0.83 residue: pdb=" N ARG B 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG B 81 " occ=0.62 residue: pdb=" N ARG C 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG C 78 " occ=0.86 residue: pdb=" N GLY C 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY C 79 " occ=0.82 residue: pdb=" N GLY C 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY C 80 " occ=0.83 residue: pdb=" N ARG C 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG C 81 " occ=0.62 ... (remaining 4 not shown) Time building chain proxies: 5.38, per 1000 atoms: 0.29 Number of scatterers: 18752 At special positions: 0 Unit cell: (130.5, 140.94, 87.696, 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 88 16.00 O 3612 8.00 N 3088 7.00 C 11964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.12 Conformation dependent library (CDL) restraints added in 954.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4408 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 18 sheets defined 43.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.572A pdb=" N PHE A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 12 " --> pdb=" O TYR A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 12' Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.080A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.598A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.561A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.747A pdb=" N ILE A 209 " --> pdb=" O VAL A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.621A pdb=" N ARG A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.611A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.650A pdb=" N GLN A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 366 removed outlier: 3.505A pdb=" N ILE A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.913A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.583A pdb=" N SER A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.646A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.639A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 12 " --> pdb=" O TYR B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 12' Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.970A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.627A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.774A pdb=" N ILE B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.597A pdb=" N ARG B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.943A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.649A pdb=" N GLN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.402A pdb=" N GLY B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.730A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 524 removed outlier: 3.615A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.673A pdb=" N ASN B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 562 through 576 removed outlier: 3.507A pdb=" N GLY B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 588 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.602A pdb=" N PHE C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 106 through 115 Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 157 through 162 removed outlier: 4.062A pdb=" N ASP C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 187 removed outlier: 3.658A pdb=" N THR C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 187 " --> pdb=" O TRP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 206 through 209 removed outlier: 3.779A pdb=" N ILE C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 209' Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.625A pdb=" N ARG C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.913A pdb=" N GLY C 330 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN C 331 " --> pdb=" O GLU C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.666A pdb=" N GLN C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 366 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.346A pdb=" N GLY C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.761A pdb=" N LEU C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 524 removed outlier: 3.617A pdb=" N SER C 511 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 537 Processing helix chain 'C' and resid 538 through 550 removed outlier: 3.687A pdb=" N ASN C 550 " --> pdb=" O ILE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 562 through 576 removed outlier: 3.641A pdb=" N LYS C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 588 Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.587A pdb=" N PHE D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 12 " --> pdb=" O TYR D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 12' Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 31 through 44 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 162 removed outlier: 4.090A pdb=" N ASP D 162 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.588A pdb=" N PHE D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.550A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 187 " --> pdb=" O TRP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE D 209 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 209' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 313 through 326 removed outlier: 3.629A pdb=" N ARG D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.638A pdb=" N GLY D 330 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 332 through 337 removed outlier: 3.642A pdb=" N GLN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 366 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.976A pdb=" N LEU D 453 " --> pdb=" O LYS D 449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 524 removed outlier: 3.566A pdb=" N SER D 511 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 537 Processing helix chain 'D' and resid 538 through 550 removed outlier: 3.642A pdb=" N ASN D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 559 Processing helix chain 'D' and resid 562 through 576 removed outlier: 3.537A pdb=" N ALA D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 574 " --> pdb=" O ALA D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.292A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 25 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 55 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 27 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER A 24 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE A 287 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 26 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 289 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 28 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.374A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 5.983A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 266 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.307A pdb=" N ILE B 52 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU B 245 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 54 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 25 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 55 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 27 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER B 24 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE B 287 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 26 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR B 289 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 28 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.474A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 257 removed outlier: 5.995A pdb=" N VAL B 250 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 270 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 252 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 266 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP B 256 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA B 264 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.300A pdb=" N ILE C 52 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 245 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 54 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 24 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE C 287 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR C 26 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR C 289 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 28 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.474A pdb=" N MET C 389 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 413 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 346 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 248 through 257 removed outlier: 5.994A pdb=" N VAL C 250 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP C 270 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP C 252 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 266 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 256 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA C 264 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB7, first strand: chain 'D' and resid 243 through 245 removed outlier: 6.261A pdb=" N ILE D 52 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU D 245 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE D 54 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA D 25 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 55 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 27 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 24 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE D 287 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR D 26 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR D 289 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 28 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET D 389 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 413 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL D 346 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 257 removed outlier: 6.016A pdb=" N VAL D 250 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP D 270 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 252 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 266 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP D 256 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA D 264 " --> pdb=" O ASP D 256 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6064 1.34 - 1.45: 3267 1.45 - 1.57: 9709 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 19184 Sorted by residual: bond pdb=" CB GLU B 110 " pdb=" CG GLU B 110 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CB GLU D 110 " pdb=" CG GLU D 110 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CG1 ILE C 427 " pdb=" CD1 ILE C 427 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 ... (remaining 19179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 25211 1.57 - 3.13: 677 3.13 - 4.70: 73 4.70 - 6.26: 33 6.26 - 7.83: 2 Bond angle restraints: 25996 Sorted by residual: angle pdb=" N VAL D 169 " pdb=" CA VAL D 169 " pdb=" C VAL D 169 " ideal model delta sigma weight residual 113.71 110.08 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" N VAL A 169 " pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 113.53 109.88 3.65 9.80e-01 1.04e+00 1.39e+01 angle pdb=" N VAL C 169 " pdb=" CA VAL C 169 " pdb=" C VAL C 169 " ideal model delta sigma weight residual 113.53 109.95 3.58 9.80e-01 1.04e+00 1.34e+01 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" C GLN C 396 " pdb=" N GLN C 397 " pdb=" CA GLN C 397 " ideal model delta sigma weight residual 121.70 127.03 -5.33 1.80e+00 3.09e-01 8.76e+00 ... (remaining 25991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 10162 14.69 - 29.38: 980 29.38 - 44.08: 269 44.08 - 58.77: 49 58.77 - 73.46: 32 Dihedral angle restraints: 11492 sinusoidal: 4672 harmonic: 6820 Sorted by residual: dihedral pdb=" CA ASP B 503 " pdb=" C ASP B 503 " pdb=" N THR B 504 " pdb=" CA THR B 504 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP C 503 " pdb=" C ASP C 503 " pdb=" N THR C 504 " pdb=" CA THR C 504 " ideal model delta harmonic sigma weight residual 180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP A 503 " pdb=" C ASP A 503 " pdb=" N THR A 504 " pdb=" CA THR A 504 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1430 0.033 - 0.067: 975 0.067 - 0.100: 284 0.100 - 0.133: 133 0.133 - 0.167: 30 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CA ILE B 380 " pdb=" N ILE B 380 " pdb=" C ILE B 380 " pdb=" CB ILE B 380 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA LYS D 589 " pdb=" N LYS D 589 " pdb=" C LYS D 589 " pdb=" CB LYS D 589 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LYS B 589 " pdb=" N LYS B 589 " pdb=" C LYS B 589 " pdb=" CB LYS B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2849 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 201 " 0.009 2.00e-02 2.50e+03 1.15e-02 2.65e+00 pdb=" CG TYR B 201 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 201 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 201 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 201 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 201 " -0.011 2.00e-02 2.50e+03 1.09e-02 2.38e+00 pdb=" CG TYR A 201 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 201 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 201 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 201 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 201 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 201 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 201 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 201 " 0.011 2.00e-02 2.50e+03 9.79e-03 1.92e+00 pdb=" CG TYR D 201 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 201 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 201 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 201 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 201 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 201 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 201 " 0.001 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4338 2.77 - 3.30: 17550 3.30 - 3.84: 32520 3.84 - 4.37: 40568 4.37 - 4.90: 67775 Nonbonded interactions: 162751 Sorted by model distance: nonbonded pdb=" OD2 ASP C 44 " pdb=" OH TYR C 520 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 44 " pdb=" OH TYR B 520 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP A 44 " pdb=" OH TYR A 520 " model vdw 2.250 3.040 nonbonded pdb=" O GLU B 356 " pdb=" OG1 THR B 360 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP D 44 " pdb=" OH TYR D 520 " model vdw 2.263 3.040 ... (remaining 162746 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.006 0.054 19184 Z= 0.277 Angle : 0.636 7.830 25996 Z= 0.353 Chirality : 0.049 0.167 2852 Planarity : 0.004 0.033 3336 Dihedral : 13.526 73.458 7084 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2300 helix: -1.11 (0.16), residues: 776 sheet: 0.07 (0.33), residues: 304 loop : -0.16 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 125 TYR 0.028 0.002 TYR B 201 PHE 0.017 0.002 PHE D 189 TRP 0.013 0.002 TRP D 91 HIS 0.005 0.001 HIS A 588 Details of bonding type rmsd covalent geometry : bond 0.00639 (19184) covalent geometry : angle 0.63637 (25996) hydrogen bonds : bond 0.23605 ( 672) hydrogen bonds : angle 7.72529 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8160 (t70) cc_final: 0.7867 (t0) REVERT: A 132 GLN cc_start: 0.8786 (mp10) cc_final: 0.8281 (mp10) REVERT: A 159 GLU cc_start: 0.9048 (mp0) cc_final: 0.8749 (mp0) REVERT: A 359 ASP cc_start: 0.9320 (m-30) cc_final: 0.9066 (m-30) REVERT: A 473 MET cc_start: 0.9491 (mmm) cc_final: 0.9189 (mmm) REVERT: A 526 ASP cc_start: 0.8557 (t70) cc_final: 0.8009 (t0) REVERT: B 82 GLU cc_start: 0.7249 (pm20) cc_final: 0.7024 (pm20) REVERT: B 88 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8844 (mm-30) REVERT: B 151 LEU cc_start: 0.8512 (mt) cc_final: 0.8262 (mp) REVERT: B 159 GLU cc_start: 0.9064 (mp0) cc_final: 0.8688 (pm20) REVERT: B 253 ILE cc_start: 0.9433 (mt) cc_final: 0.9194 (mp) REVERT: B 401 ASP cc_start: 0.8711 (m-30) cc_final: 0.8404 (p0) REVERT: C 82 GLU cc_start: 0.7268 (pm20) cc_final: 0.7034 (pm20) REVERT: C 159 GLU cc_start: 0.9065 (mp0) cc_final: 0.8789 (pm20) REVERT: C 253 ILE cc_start: 0.9424 (mt) cc_final: 0.9179 (mp) REVERT: D 117 GLU cc_start: 0.9094 (pt0) cc_final: 0.8604 (pp20) REVERT: D 132 GLN cc_start: 0.8862 (mp10) cc_final: 0.8330 (mp10) REVERT: D 159 GLU cc_start: 0.9085 (mp0) cc_final: 0.8713 (mp0) REVERT: D 359 ASP cc_start: 0.9319 (m-30) cc_final: 0.9061 (m-30) REVERT: D 452 ASP cc_start: 0.8904 (p0) cc_final: 0.8351 (t0) REVERT: D 473 MET cc_start: 0.9488 (mmm) cc_final: 0.9210 (mmm) REVERT: D 534 ASN cc_start: 0.9547 (p0) cc_final: 0.9096 (p0) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 0.7826 time to fit residues: 192.8370 Evaluate side-chains 114 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0070 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 22 ASN B 240 HIS B 442 HIS C 22 ASN C 240 HIS C 442 HIS C 486 HIS D 240 HIS D 331 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059963 restraints weight = 40839.883| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.14 r_work: 0.2689 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19184 Z= 0.108 Angle : 0.499 6.457 25996 Z= 0.266 Chirality : 0.043 0.159 2852 Planarity : 0.003 0.034 3336 Dihedral : 4.209 16.637 2506 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.62 % Allowed : 7.69 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 2300 helix: 0.32 (0.18), residues: 796 sheet: 0.21 (0.33), residues: 284 loop : 0.10 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 324 TYR 0.012 0.001 TYR D 112 PHE 0.020 0.001 PHE A 506 TRP 0.004 0.001 TRP D 183 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00247 (19184) covalent geometry : angle 0.49855 (25996) hydrogen bonds : bond 0.03712 ( 672) hydrogen bonds : angle 4.63782 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8837 (mp10) cc_final: 0.8236 (mp10) REVERT: A 159 GLU cc_start: 0.9142 (mp0) cc_final: 0.8912 (mp0) REVERT: A 359 ASP cc_start: 0.9233 (m-30) cc_final: 0.8930 (m-30) REVERT: A 430 CYS cc_start: 0.9001 (m) cc_final: 0.8378 (m) REVERT: A 473 MET cc_start: 0.9430 (mmm) cc_final: 0.9116 (mmm) REVERT: A 526 ASP cc_start: 0.8793 (t70) cc_final: 0.8571 (p0) REVERT: A 557 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8281 (mp0) REVERT: B 159 GLU cc_start: 0.9182 (mp0) cc_final: 0.8950 (pm20) REVERT: B 401 ASP cc_start: 0.8868 (m-30) cc_final: 0.8437 (p0) REVERT: B 564 MET cc_start: 0.8971 (mmm) cc_final: 0.8543 (tmt) REVERT: B 583 SER cc_start: 0.8543 (m) cc_final: 0.8319 (p) REVERT: C 253 ILE cc_start: 0.9412 (mt) cc_final: 0.9097 (mm) REVERT: C 583 SER cc_start: 0.8496 (m) cc_final: 0.8278 (p) REVERT: D 132 GLN cc_start: 0.8894 (mp10) cc_final: 0.8257 (mp10) REVERT: D 159 GLU cc_start: 0.9179 (mp0) cc_final: 0.8837 (mp0) REVERT: D 359 ASP cc_start: 0.9235 (m-30) cc_final: 0.8936 (m-30) REVERT: D 430 CYS cc_start: 0.9042 (m) cc_final: 0.8420 (m) REVERT: D 452 ASP cc_start: 0.8854 (p0) cc_final: 0.8449 (t0) REVERT: D 473 MET cc_start: 0.9431 (mmm) cc_final: 0.9143 (mmm) REVERT: D 557 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8030 (mp0) outliers start: 13 outliers final: 4 residues processed: 167 average time/residue: 0.6532 time to fit residues: 120.7082 Evaluate side-chains 109 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 508 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 197 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 149 optimal weight: 0.0570 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059937 restraints weight = 41220.528| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.16 r_work: 0.2674 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19184 Z= 0.104 Angle : 0.461 5.597 25996 Z= 0.245 Chirality : 0.042 0.238 2852 Planarity : 0.003 0.031 3336 Dihedral : 3.887 16.550 2504 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.20 % Allowed : 9.66 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2300 helix: 0.99 (0.19), residues: 796 sheet: 0.20 (0.33), residues: 284 loop : 0.21 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 324 TYR 0.013 0.001 TYR D 112 PHE 0.025 0.001 PHE D 506 TRP 0.004 0.001 TRP C 192 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00238 (19184) covalent geometry : angle 0.46102 (25996) hydrogen bonds : bond 0.03116 ( 672) hydrogen bonds : angle 4.20826 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8865 (mp10) cc_final: 0.8212 (mp10) REVERT: A 159 GLU cc_start: 0.9194 (mp0) cc_final: 0.8990 (mp0) REVERT: A 198 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8505 (ttt) REVERT: A 359 ASP cc_start: 0.9203 (m-30) cc_final: 0.8905 (m-30) REVERT: A 430 CYS cc_start: 0.9002 (m) cc_final: 0.8438 (m) REVERT: A 473 MET cc_start: 0.9458 (mmm) cc_final: 0.9173 (mmm) REVERT: A 526 ASP cc_start: 0.8781 (t70) cc_final: 0.8561 (p0) REVERT: A 557 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8314 (mp0) REVERT: B 253 ILE cc_start: 0.9412 (mt) cc_final: 0.9210 (mp) REVERT: B 401 ASP cc_start: 0.8817 (m-30) cc_final: 0.8415 (p0) REVERT: B 471 TYR cc_start: 0.8872 (p90) cc_final: 0.8626 (p90) REVERT: B 506 PHE cc_start: 0.8836 (t80) cc_final: 0.8614 (t80) REVERT: C 151 LEU cc_start: 0.8707 (mm) cc_final: 0.8219 (tp) REVERT: C 198 MET cc_start: 0.9303 (tpp) cc_final: 0.8964 (tpt) REVERT: C 471 TYR cc_start: 0.8908 (p90) cc_final: 0.8680 (p90) REVERT: D 84 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7306 (pp20) REVERT: D 132 GLN cc_start: 0.8894 (mp10) cc_final: 0.8210 (mp10) REVERT: D 159 GLU cc_start: 0.9197 (mp0) cc_final: 0.8935 (mp0) REVERT: D 222 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7830 (ttpt) REVERT: D 359 ASP cc_start: 0.9155 (m-30) cc_final: 0.8806 (m-30) REVERT: D 430 CYS cc_start: 0.9041 (m) cc_final: 0.8462 (m) REVERT: D 452 ASP cc_start: 0.8793 (p0) cc_final: 0.8421 (t0) REVERT: D 473 MET cc_start: 0.9440 (mmm) cc_final: 0.9155 (mmm) REVERT: D 526 ASP cc_start: 0.8506 (p0) cc_final: 0.8135 (p0) REVERT: D 557 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8225 (mp0) REVERT: D 564 MET cc_start: 0.8332 (pmm) cc_final: 0.8100 (tmm) outliers start: 25 outliers final: 4 residues processed: 143 average time/residue: 0.5865 time to fit residues: 94.1929 Evaluate side-chains 109 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 222 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 98 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 206 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059024 restraints weight = 40706.996| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.15 r_work: 0.2676 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19184 Z= 0.096 Angle : 0.441 6.972 25996 Z= 0.234 Chirality : 0.042 0.173 2852 Planarity : 0.003 0.032 3336 Dihedral : 3.738 17.213 2504 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.25 % Allowed : 10.87 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2300 helix: 1.26 (0.19), residues: 796 sheet: -0.08 (0.32), residues: 304 loop : 0.33 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 324 TYR 0.013 0.001 TYR D 112 PHE 0.022 0.001 PHE A 506 TRP 0.004 0.001 TRP C 192 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00221 (19184) covalent geometry : angle 0.44112 (25996) hydrogen bonds : bond 0.02781 ( 672) hydrogen bonds : angle 4.02562 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8871 (mp10) cc_final: 0.8157 (mp10) REVERT: A 159 GLU cc_start: 0.9191 (mp0) cc_final: 0.8976 (mp0) REVERT: A 198 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8293 (ttt) REVERT: A 430 CYS cc_start: 0.8956 (m) cc_final: 0.8433 (m) REVERT: A 465 MET cc_start: 0.9583 (mtm) cc_final: 0.9223 (mtm) REVERT: A 473 MET cc_start: 0.9446 (mmm) cc_final: 0.9169 (mmm) REVERT: A 526 ASP cc_start: 0.8856 (t70) cc_final: 0.8515 (p0) REVERT: A 557 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8298 (mp0) REVERT: B 253 ILE cc_start: 0.9383 (mt) cc_final: 0.9170 (mp) REVERT: B 401 ASP cc_start: 0.8817 (m-30) cc_final: 0.8403 (p0) REVERT: B 451 GLU cc_start: 0.9137 (tt0) cc_final: 0.8791 (tm-30) REVERT: B 471 TYR cc_start: 0.8861 (p90) cc_final: 0.8476 (p90) REVERT: B 506 PHE cc_start: 0.8794 (t80) cc_final: 0.8504 (t80) REVERT: B 526 ASP cc_start: 0.8337 (t70) cc_final: 0.7896 (t0) REVERT: C 198 MET cc_start: 0.9324 (tpp) cc_final: 0.9065 (tpt) REVERT: C 253 ILE cc_start: 0.9372 (mt) cc_final: 0.9101 (mm) REVERT: C 451 GLU cc_start: 0.9136 (tt0) cc_final: 0.8813 (tm-30) REVERT: D 83 MET cc_start: 0.7710 (mtm) cc_final: 0.7435 (mtm) REVERT: D 84 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: D 132 GLN cc_start: 0.8892 (mp10) cc_final: 0.8180 (mp10) REVERT: D 222 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7692 (ttpt) REVERT: D 245 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: D 359 ASP cc_start: 0.9157 (m-30) cc_final: 0.8806 (m-30) REVERT: D 430 CYS cc_start: 0.9003 (m) cc_final: 0.8469 (m) REVERT: D 473 MET cc_start: 0.9435 (mmm) cc_final: 0.9157 (mmm) REVERT: D 526 ASP cc_start: 0.8531 (p0) cc_final: 0.8229 (p0) outliers start: 26 outliers final: 3 residues processed: 140 average time/residue: 0.5597 time to fit residues: 87.2697 Evaluate side-chains 105 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 0 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN B 486 HIS ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.055179 restraints weight = 41323.689| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.14 r_work: 0.2582 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19184 Z= 0.184 Angle : 0.497 7.462 25996 Z= 0.262 Chirality : 0.044 0.152 2852 Planarity : 0.003 0.036 3336 Dihedral : 3.942 17.456 2504 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.35 % Allowed : 11.11 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2300 helix: 1.33 (0.19), residues: 796 sheet: -0.12 (0.32), residues: 304 loop : 0.32 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 527 TYR 0.016 0.001 TYR C 471 PHE 0.028 0.001 PHE A 506 TRP 0.005 0.001 TRP C 113 HIS 0.004 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00424 (19184) covalent geometry : angle 0.49682 (25996) hydrogen bonds : bond 0.03081 ( 672) hydrogen bonds : angle 4.07873 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8876 (mp10) cc_final: 0.8166 (mp10) REVERT: A 159 GLU cc_start: 0.9258 (mp0) cc_final: 0.9019 (mp0) REVERT: A 198 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8605 (ttt) REVERT: A 430 CYS cc_start: 0.9054 (m) cc_final: 0.8615 (m) REVERT: A 437 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: A 465 MET cc_start: 0.9620 (mtm) cc_final: 0.9231 (mtm) REVERT: A 473 MET cc_start: 0.9422 (mmm) cc_final: 0.9188 (mmm) REVERT: A 526 ASP cc_start: 0.8981 (t70) cc_final: 0.8445 (p0) REVERT: B 253 ILE cc_start: 0.9380 (mt) cc_final: 0.9116 (mm) REVERT: B 401 ASP cc_start: 0.8795 (m-30) cc_final: 0.8461 (p0) REVERT: B 526 ASP cc_start: 0.8497 (t70) cc_final: 0.7972 (t0) REVERT: C 198 MET cc_start: 0.9358 (tpp) cc_final: 0.9118 (tpt) REVERT: C 253 ILE cc_start: 0.9381 (mt) cc_final: 0.9119 (mm) REVERT: D 83 MET cc_start: 0.7806 (mtm) cc_final: 0.7479 (mtm) REVERT: D 84 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7281 (pp20) REVERT: D 132 GLN cc_start: 0.8890 (mp10) cc_final: 0.8175 (mp10) REVERT: D 355 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8684 (mmmm) REVERT: D 359 ASP cc_start: 0.9175 (m-30) cc_final: 0.8831 (m-30) REVERT: D 430 CYS cc_start: 0.9085 (m) cc_final: 0.8635 (m) REVERT: D 437 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: D 465 MET cc_start: 0.9653 (mtm) cc_final: 0.9271 (mtm) REVERT: D 473 MET cc_start: 0.9414 (mmm) cc_final: 0.9186 (mmm) REVERT: D 526 ASP cc_start: 0.8597 (p0) cc_final: 0.8311 (p0) REVERT: D 564 MET cc_start: 0.8381 (pmm) cc_final: 0.8087 (tmm) outliers start: 28 outliers final: 7 residues processed: 119 average time/residue: 0.5900 time to fit residues: 78.5084 Evaluate side-chains 102 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 184 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 0 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 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 = 0.3142 r_free = 0.3142 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056853 restraints weight = 40594.879| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.13 r_work: 0.2614 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19184 Z= 0.123 Angle : 0.457 7.926 25996 Z= 0.241 Chirality : 0.042 0.147 2852 Planarity : 0.003 0.035 3336 Dihedral : 3.814 18.626 2504 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.82 % Allowed : 11.68 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2300 helix: 1.42 (0.19), residues: 796 sheet: -0.13 (0.32), residues: 304 loop : 0.38 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 324 TYR 0.012 0.001 TYR B 471 PHE 0.020 0.001 PHE A 506 TRP 0.003 0.001 TRP C 344 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00286 (19184) covalent geometry : angle 0.45659 (25996) hydrogen bonds : bond 0.02763 ( 672) hydrogen bonds : angle 3.96975 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7805 (mtm) cc_final: 0.7409 (mtm) REVERT: A 132 GLN cc_start: 0.8875 (mp10) cc_final: 0.8151 (mp10) REVERT: A 159 GLU cc_start: 0.9250 (mp0) cc_final: 0.9022 (mp0) REVERT: A 198 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8555 (ttt) REVERT: A 430 CYS cc_start: 0.9034 (m) cc_final: 0.8493 (m) REVERT: A 465 MET cc_start: 0.9605 (mtm) cc_final: 0.9319 (mtm) REVERT: A 473 MET cc_start: 0.9406 (mmm) cc_final: 0.9178 (mmm) REVERT: A 526 ASP cc_start: 0.8959 (t70) cc_final: 0.8409 (p0) REVERT: A 557 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8364 (mp0) REVERT: A 564 MET cc_start: 0.8635 (pmm) cc_final: 0.8321 (tmm) REVERT: B 253 ILE cc_start: 0.9378 (mt) cc_final: 0.9107 (mm) REVERT: B 401 ASP cc_start: 0.8788 (m-30) cc_final: 0.8390 (p0) REVERT: B 526 ASP cc_start: 0.8548 (t70) cc_final: 0.8023 (t0) REVERT: C 198 MET cc_start: 0.9353 (tpp) cc_final: 0.9113 (tpt) REVERT: C 253 ILE cc_start: 0.9393 (mt) cc_final: 0.9127 (mm) REVERT: C 465 MET cc_start: 0.9581 (mtm) cc_final: 0.9308 (mtm) REVERT: D 84 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: D 132 GLN cc_start: 0.8895 (mp10) cc_final: 0.8184 (mp10) REVERT: D 198 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8551 (ttt) REVERT: D 355 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8409 (tppp) REVERT: D 359 ASP cc_start: 0.9169 (m-30) cc_final: 0.8768 (m-30) REVERT: D 430 CYS cc_start: 0.9060 (m) cc_final: 0.8519 (m) REVERT: D 465 MET cc_start: 0.9638 (mtm) cc_final: 0.9283 (mtm) REVERT: D 473 MET cc_start: 0.9404 (mmm) cc_final: 0.9190 (mmm) REVERT: D 526 ASP cc_start: 0.8569 (p0) cc_final: 0.8214 (p0) REVERT: D 557 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8318 (mp0) REVERT: D 564 MET cc_start: 0.8377 (pmm) cc_final: 0.7980 (tmm) outliers start: 17 outliers final: 5 residues processed: 113 average time/residue: 0.5959 time to fit residues: 75.1206 Evaluate side-chains 101 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 150 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 0 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 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 = 0.3127 r_free = 0.3127 target = 0.073831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.056152 restraints weight = 41182.891| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.12 r_work: 0.2595 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19184 Z= 0.153 Angle : 0.473 8.993 25996 Z= 0.250 Chirality : 0.043 0.148 2852 Planarity : 0.003 0.048 3336 Dihedral : 3.866 18.743 2504 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.96 % Allowed : 11.54 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2300 helix: 1.46 (0.19), residues: 796 sheet: -0.17 (0.32), residues: 304 loop : 0.39 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 81 TYR 0.013 0.001 TYR D 236 PHE 0.036 0.001 PHE C 506 TRP 0.004 0.001 TRP C 344 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00356 (19184) covalent geometry : angle 0.47292 (25996) hydrogen bonds : bond 0.02854 ( 672) hydrogen bonds : angle 3.98011 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8845 (mp10) cc_final: 0.8129 (mp10) REVERT: A 159 GLU cc_start: 0.9264 (mp0) cc_final: 0.9033 (mp0) REVERT: A 198 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8578 (ttt) REVERT: A 401 ASP cc_start: 0.8515 (t0) cc_final: 0.8265 (t0) REVERT: A 430 CYS cc_start: 0.9066 (m) cc_final: 0.8553 (m) REVERT: A 465 MET cc_start: 0.9625 (mtm) cc_final: 0.9346 (mtm) REVERT: A 473 MET cc_start: 0.9402 (mmm) cc_final: 0.9168 (mmm) REVERT: A 526 ASP cc_start: 0.8979 (t70) cc_final: 0.8445 (p0) REVERT: A 557 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8359 (mp0) REVERT: B 253 ILE cc_start: 0.9371 (mt) cc_final: 0.9099 (mm) REVERT: B 401 ASP cc_start: 0.8836 (m-30) cc_final: 0.8484 (p0) REVERT: B 526 ASP cc_start: 0.8578 (t70) cc_final: 0.8057 (t0) REVERT: C 198 MET cc_start: 0.9367 (tpp) cc_final: 0.9132 (tpt) REVERT: C 253 ILE cc_start: 0.9389 (mt) cc_final: 0.9121 (mm) REVERT: C 465 MET cc_start: 0.9571 (mtm) cc_final: 0.9284 (mtm) REVERT: D 0 HIS cc_start: 0.8546 (m-70) cc_final: 0.8212 (m-70) REVERT: D 84 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: D 132 GLN cc_start: 0.8894 (mp10) cc_final: 0.8209 (mp10) REVERT: D 198 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8537 (ttt) REVERT: D 355 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8423 (tppp) REVERT: D 359 ASP cc_start: 0.9162 (m-30) cc_final: 0.8763 (m-30) REVERT: D 430 CYS cc_start: 0.9074 (m) cc_final: 0.8560 (m) REVERT: D 437 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: D 465 MET cc_start: 0.9631 (mtm) cc_final: 0.9284 (mtm) REVERT: D 473 MET cc_start: 0.9412 (mmm) cc_final: 0.9198 (mmm) REVERT: D 526 ASP cc_start: 0.8589 (p0) cc_final: 0.8298 (p0) REVERT: D 557 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8330 (mp0) REVERT: D 564 MET cc_start: 0.8380 (pmm) cc_final: 0.8009 (tmm) outliers start: 20 outliers final: 9 residues processed: 115 average time/residue: 0.5712 time to fit residues: 73.2511 Evaluate side-chains 108 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 0 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN ** D 437 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 = 0.3087 r_free = 0.3087 target = 0.072120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.054052 restraints weight = 41676.363| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.21 r_work: 0.2545 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 19184 Z= 0.243 Angle : 0.535 9.846 25996 Z= 0.282 Chirality : 0.045 0.153 2852 Planarity : 0.003 0.036 3336 Dihedral : 4.113 18.903 2504 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.11 % Allowed : 11.83 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2300 helix: 1.42 (0.19), residues: 796 sheet: -0.37 (0.31), residues: 304 loop : 0.31 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 81 TYR 0.017 0.002 TYR A 236 PHE 0.048 0.001 PHE B 506 TRP 0.007 0.001 TRP C 113 HIS 0.005 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00561 (19184) covalent geometry : angle 0.53452 (25996) hydrogen bonds : bond 0.03186 ( 672) hydrogen bonds : angle 4.14247 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7874 (mtm) cc_final: 0.7385 (mtm) REVERT: A 132 GLN cc_start: 0.8847 (mp10) cc_final: 0.8155 (mp10) REVERT: A 159 GLU cc_start: 0.9271 (mp0) cc_final: 0.9039 (mp0) REVERT: A 198 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8641 (ttt) REVERT: A 203 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: A 430 CYS cc_start: 0.9096 (m) cc_final: 0.8596 (m) REVERT: A 437 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: A 465 MET cc_start: 0.9628 (mtm) cc_final: 0.9270 (mtm) REVERT: A 473 MET cc_start: 0.9390 (mmm) cc_final: 0.9149 (mmm) REVERT: A 526 ASP cc_start: 0.9014 (t70) cc_final: 0.8308 (p0) REVERT: A 564 MET cc_start: 0.8595 (pmm) cc_final: 0.8305 (tmm) REVERT: B 253 ILE cc_start: 0.9367 (mt) cc_final: 0.9091 (mm) REVERT: B 401 ASP cc_start: 0.8890 (m-30) cc_final: 0.8588 (p0) REVERT: B 526 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 253 ILE cc_start: 0.9370 (mt) cc_final: 0.9096 (mm) REVERT: C 465 MET cc_start: 0.9560 (mtm) cc_final: 0.9255 (mtm) REVERT: D 83 MET cc_start: 0.7960 (mtm) cc_final: 0.7504 (mtm) REVERT: D 84 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: D 132 GLN cc_start: 0.8865 (mp10) cc_final: 0.8185 (mp10) REVERT: D 198 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8588 (ttt) REVERT: D 355 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8408 (tppp) REVERT: D 359 ASP cc_start: 0.9202 (m-30) cc_final: 0.8799 (m-30) REVERT: D 430 CYS cc_start: 0.9135 (m) cc_final: 0.8626 (m) REVERT: D 437 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: D 465 MET cc_start: 0.9627 (mtm) cc_final: 0.9328 (mtm) REVERT: D 473 MET cc_start: 0.9390 (mmm) cc_final: 0.9166 (mmm) REVERT: D 526 ASP cc_start: 0.8595 (p0) cc_final: 0.8381 (p0) REVERT: D 564 MET cc_start: 0.8408 (pmm) cc_final: 0.8041 (tmm) outliers start: 23 outliers final: 7 residues processed: 108 average time/residue: 0.5951 time to fit residues: 72.2476 Evaluate side-chains 102 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 136 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 165 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN ** D 437 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 = 0.3159 r_free = 0.3159 target = 0.075408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057620 restraints weight = 40654.522| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.14 r_work: 0.2634 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19184 Z= 0.095 Angle : 0.462 8.845 25996 Z= 0.246 Chirality : 0.042 0.164 2852 Planarity : 0.003 0.060 3336 Dihedral : 3.806 19.383 2504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.53 % Allowed : 12.50 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.18), residues: 2300 helix: 1.55 (0.19), residues: 796 sheet: -0.31 (0.31), residues: 304 loop : 0.41 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 81 TYR 0.020 0.001 TYR C 471 PHE 0.032 0.001 PHE B 506 TRP 0.006 0.001 TRP C 183 HIS 0.002 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00219 (19184) covalent geometry : angle 0.46248 (25996) hydrogen bonds : bond 0.02661 ( 672) hydrogen bonds : angle 3.96622 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7856 (mtm) cc_final: 0.7259 (mtm) REVERT: A 132 GLN cc_start: 0.8881 (mp10) cc_final: 0.8182 (mp10) REVERT: A 159 GLU cc_start: 0.9273 (mp0) cc_final: 0.9068 (mp0) REVERT: A 198 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8493 (ttt) REVERT: A 203 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: A 401 ASP cc_start: 0.8477 (t0) cc_final: 0.8234 (t0) REVERT: A 430 CYS cc_start: 0.8996 (m) cc_final: 0.8421 (m) REVERT: A 465 MET cc_start: 0.9590 (mtm) cc_final: 0.9266 (mtm) REVERT: A 473 MET cc_start: 0.9385 (mmm) cc_final: 0.9162 (mmm) REVERT: A 526 ASP cc_start: 0.8961 (t70) cc_final: 0.8333 (p0) REVERT: A 557 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8372 (mp0) REVERT: A 564 MET cc_start: 0.8554 (pmm) cc_final: 0.8269 (tmm) REVERT: B 253 ILE cc_start: 0.9380 (mt) cc_final: 0.9102 (mm) REVERT: B 401 ASP cc_start: 0.8716 (m-30) cc_final: 0.8335 (p0) REVERT: B 526 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8152 (t0) REVERT: C 253 ILE cc_start: 0.9395 (mt) cc_final: 0.9121 (mm) REVERT: D 0 HIS cc_start: 0.8515 (m-70) cc_final: 0.8087 (m-70) REVERT: D 83 MET cc_start: 0.7860 (mtm) cc_final: 0.7317 (mtm) REVERT: D 84 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: D 132 GLN cc_start: 0.8885 (mp10) cc_final: 0.8206 (mp10) REVERT: D 198 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8496 (ttt) REVERT: D 355 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8375 (tppp) REVERT: D 359 ASP cc_start: 0.9147 (m-30) cc_final: 0.8732 (m-30) REVERT: D 430 CYS cc_start: 0.9011 (m) cc_final: 0.8449 (m) REVERT: D 465 MET cc_start: 0.9594 (mtm) cc_final: 0.9300 (mtm) REVERT: D 473 MET cc_start: 0.9383 (mmm) cc_final: 0.9160 (mmm) REVERT: D 526 ASP cc_start: 0.8534 (p0) cc_final: 0.8187 (p0) REVERT: D 557 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8384 (mp0) REVERT: D 564 MET cc_start: 0.8380 (pmm) cc_final: 0.8050 (tmm) outliers start: 11 outliers final: 5 residues processed: 111 average time/residue: 0.5884 time to fit residues: 73.2733 Evaluate side-chains 107 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN ** D 437 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 = 0.3096 r_free = 0.3096 target = 0.072662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.054557 restraints weight = 41634.697| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.22 r_work: 0.2554 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 19184 Z= 0.223 Angle : 0.535 9.977 25996 Z= 0.284 Chirality : 0.045 0.153 2852 Planarity : 0.004 0.078 3336 Dihedral : 4.080 19.107 2504 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.67 % Allowed : 12.16 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2300 helix: 1.47 (0.19), residues: 796 sheet: -0.42 (0.31), residues: 304 loop : 0.38 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 81 TYR 0.020 0.001 TYR D 471 PHE 0.041 0.001 PHE C 506 TRP 0.007 0.001 TRP C 113 HIS 0.004 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00517 (19184) covalent geometry : angle 0.53481 (25996) hydrogen bonds : bond 0.03098 ( 672) hydrogen bonds : angle 4.14447 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8833 (mp10) cc_final: 0.8140 (mp10) REVERT: A 159 GLU cc_start: 0.9275 (mp0) cc_final: 0.9045 (mp0) REVERT: A 198 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8626 (ttt) REVERT: A 203 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: A 401 ASP cc_start: 0.8578 (t0) cc_final: 0.8312 (t0) REVERT: A 430 CYS cc_start: 0.9109 (m) cc_final: 0.8610 (m) REVERT: A 437 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: A 465 MET cc_start: 0.9615 (mtm) cc_final: 0.9261 (mtm) REVERT: A 473 MET cc_start: 0.9373 (mmm) cc_final: 0.9137 (mmm) REVERT: A 526 ASP cc_start: 0.8990 (t70) cc_final: 0.8304 (p0) REVERT: A 564 MET cc_start: 0.8593 (pmm) cc_final: 0.8215 (tmm) REVERT: B 253 ILE cc_start: 0.9367 (mt) cc_final: 0.9088 (mm) REVERT: B 401 ASP cc_start: 0.8855 (m-30) cc_final: 0.8497 (p0) REVERT: B 526 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8257 (t0) REVERT: C 253 ILE cc_start: 0.9381 (mt) cc_final: 0.9108 (mm) REVERT: C 465 MET cc_start: 0.9306 (mtp) cc_final: 0.9043 (mtp) REVERT: D 81 ARG cc_start: 0.7218 (ppt-90) cc_final: 0.6940 (ptt180) REVERT: D 83 MET cc_start: 0.7847 (mtm) cc_final: 0.7501 (mtm) REVERT: D 84 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7320 (pp20) REVERT: D 132 GLN cc_start: 0.8825 (mp10) cc_final: 0.8128 (mp10) REVERT: D 198 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8567 (ttt) REVERT: D 355 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8423 (tppp) REVERT: D 359 ASP cc_start: 0.9198 (m-30) cc_final: 0.8785 (m-30) REVERT: D 430 CYS cc_start: 0.9084 (m) cc_final: 0.8598 (m) REVERT: D 437 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: D 465 MET cc_start: 0.9609 (mtm) cc_final: 0.9315 (mtm) REVERT: D 473 MET cc_start: 0.9383 (mmm) cc_final: 0.9168 (mmm) REVERT: D 526 ASP cc_start: 0.8600 (p0) cc_final: 0.8380 (p0) REVERT: D 564 MET cc_start: 0.8415 (pmm) cc_final: 0.8071 (tmm) outliers start: 14 outliers final: 3 residues processed: 101 average time/residue: 0.6712 time to fit residues: 76.2904 Evaluate side-chains 102 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 217 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 43 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.059654 restraints weight = 41036.999| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.14 r_work: 0.2652 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19184 Z= 0.089 Angle : 0.464 10.008 25996 Z= 0.246 Chirality : 0.042 0.143 2852 Planarity : 0.003 0.064 3336 Dihedral : 3.781 19.421 2504 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.48 % Allowed : 12.36 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2300 helix: 1.60 (0.19), residues: 796 sheet: -0.30 (0.31), residues: 304 loop : 0.44 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 81 TYR 0.025 0.001 TYR C 471 PHE 0.026 0.001 PHE B 506 TRP 0.007 0.001 TRP C 183 HIS 0.002 0.001 HIS C 552 Details of bonding type rmsd covalent geometry : bond 0.00203 (19184) covalent geometry : angle 0.46386 (25996) hydrogen bonds : bond 0.02592 ( 672) hydrogen bonds : angle 3.94408 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.14 seconds wall clock time: 68 minutes 37.25 seconds (4117.25 seconds total)