Starting phenix.real_space_refine on Mon Jun 16 15:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ur8_42487/06_2025/8ur8_42487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ur8_42487/06_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_42487/06_2025/8ur8_42487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ur8_42487/06_2025/8ur8_42487.map" model { file = "/net/cci-nas-00/data/ceres_data/8ur8_42487/06_2025/8ur8_42487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ur8_42487/06_2025/8ur8_42487.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.85, per 1000 atoms: 0.58 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: 4.27 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.06 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: 6.01 Time building geometry restraints manager: 5.12 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: 0.04 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: 0.750 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.420 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.170 ------------------------------------------------------------------------------- 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 : 4.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP D 91 HIS 0.005 0.001 HIS A 588 PHE 0.017 0.002 PHE D 189 TYR 0.028 0.002 TYR B 201 ARG 0.004 0.001 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.23605 ( 672) hydrogen bonds : angle 7.72529 ( 1869) covalent geometry : bond 0.00639 (19184) covalent geometry : angle 0.63637 (25996) *********************** 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 : 2.281 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 159 GLU cc_start: 0.9065 (mp0) cc_final: 0.8789 (pm20) REVERT: C 253 ILE cc_start: 0.9424 (mt) cc_final: 0.9178 (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: 1.8431 time to fit residues: 454.9732 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 : 2.204 ------------------------------------------------------------------------------- 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 192 optimal weight: 1.9990 chunk 172 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.076347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.058988 restraints weight = 40922.586| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.14 r_work: 0.2666 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19184 Z= 0.128 Angle : 0.508 6.303 25996 Z= 0.271 Chirality : 0.043 0.161 2852 Planarity : 0.003 0.034 3336 Dihedral : 4.262 16.621 2506 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.82 % Allowed : 7.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2300 helix: 0.32 (0.18), residues: 796 sheet: 0.20 (0.33), residues: 284 loop : 0.09 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 192 HIS 0.003 0.001 HIS A 588 PHE 0.023 0.001 PHE A 506 TYR 0.011 0.001 TYR B 223 ARG 0.011 0.001 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 672) hydrogen bonds : angle 4.64578 ( 1869) covalent geometry : bond 0.00292 (19184) covalent geometry : angle 0.50832 (25996) *********************** 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 161 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 2.284 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: 0.8845 (mp10) cc_final: 0.8231 (mp10) REVERT: A 159 GLU cc_start: 0.9165 (mp0) cc_final: 0.8929 (mp0) REVERT: A 359 ASP cc_start: 0.9235 (m-30) cc_final: 0.8944 (m-30) REVERT: A 430 CYS cc_start: 0.9023 (m) cc_final: 0.8428 (m) REVERT: A 473 MET cc_start: 0.9431 (mmm) cc_final: 0.9118 (mmm) REVERT: A 526 ASP cc_start: 0.8829 (t70) cc_final: 0.8485 (p0) REVERT: A 557 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8300 (mp0) REVERT: B 159 GLU cc_start: 0.9177 (mp0) cc_final: 0.8927 (pm20) REVERT: B 401 ASP cc_start: 0.8848 (m-30) cc_final: 0.8435 (p0) REVERT: B 564 MET cc_start: 0.8956 (mmm) cc_final: 0.8518 (tmt) REVERT: B 583 SER cc_start: 0.8546 (m) cc_final: 0.8316 (p) REVERT: C 253 ILE cc_start: 0.9408 (mt) cc_final: 0.9093 (mm) REVERT: C 583 SER cc_start: 0.8507 (m) cc_final: 0.8282 (p) REVERT: D 132 GLN cc_start: 0.8896 (mp10) cc_final: 0.8277 (mp10) REVERT: D 159 GLU cc_start: 0.9187 (mp0) cc_final: 0.8843 (mp0) REVERT: D 359 ASP cc_start: 0.9236 (m-30) cc_final: 0.8941 (m-30) REVERT: D 430 CYS cc_start: 0.9078 (m) cc_final: 0.8476 (m) REVERT: D 452 ASP cc_start: 0.8854 (p0) cc_final: 0.8446 (t0) REVERT: D 473 MET cc_start: 0.9431 (mmm) cc_final: 0.9141 (mmm) REVERT: D 557 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8053 (mp0) outliers start: 17 outliers final: 4 residues processed: 156 average time/residue: 1.5655 time to fit residues: 271.3109 Evaluate side-chains 115 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055864 restraints weight = 41046.197| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.10 r_work: 0.2603 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1954 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= 0.185 Angle : 0.503 5.729 25996 Z= 0.268 Chirality : 0.044 0.158 2852 Planarity : 0.003 0.030 3336 Dihedral : 4.154 16.766 2504 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.06 % Allowed : 9.62 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2300 helix: 0.95 (0.19), residues: 796 sheet: -0.17 (0.32), residues: 304 loop : 0.19 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 344 HIS 0.004 0.001 HIS C 588 PHE 0.025 0.001 PHE A 506 TYR 0.015 0.001 TYR D 236 ARG 0.006 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 672) hydrogen bonds : angle 4.33791 ( 1869) covalent geometry : bond 0.00425 (19184) covalent geometry : angle 0.50299 (25996) *********************** 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 136 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8857 (mp10) cc_final: 0.8179 (mp10) REVERT: A 159 GLU cc_start: 0.9236 (mp0) cc_final: 0.8987 (mp0) REVERT: A 359 ASP cc_start: 0.9207 (m-30) cc_final: 0.8945 (m-30) REVERT: A 430 CYS cc_start: 0.9091 (m) cc_final: 0.8545 (m) REVERT: A 473 MET cc_start: 0.9418 (mmm) cc_final: 0.9170 (mmm) REVERT: A 526 ASP cc_start: 0.8832 (t70) cc_final: 0.8424 (p0) REVERT: A 557 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8363 (mp0) REVERT: B 47 MET cc_start: 0.8447 (ttm) cc_final: 0.8245 (ttp) REVERT: B 159 GLU cc_start: 0.9158 (mp0) cc_final: 0.8938 (pm20) REVERT: B 401 ASP cc_start: 0.8831 (m-30) cc_final: 0.8427 (p0) REVERT: C 82 GLU cc_start: 0.7655 (pm20) cc_final: 0.7345 (pm20) REVERT: C 253 ILE cc_start: 0.9383 (mt) cc_final: 0.9146 (mm) REVERT: D 132 GLN cc_start: 0.8860 (mp10) cc_final: 0.8145 (mp10) REVERT: D 159 GLU cc_start: 0.9174 (mp0) cc_final: 0.8854 (mp0) REVERT: D 359 ASP cc_start: 0.9194 (m-30) cc_final: 0.8858 (m-30) REVERT: D 430 CYS cc_start: 0.9125 (m) cc_final: 0.8565 (m) REVERT: D 473 MET cc_start: 0.9376 (mmm) cc_final: 0.9142 (mmm) REVERT: D 526 ASP cc_start: 0.8554 (p0) cc_final: 0.8229 (p0) REVERT: D 564 MET cc_start: 0.8403 (pmm) cc_final: 0.8148 (tmm) outliers start: 22 outliers final: 5 residues processed: 131 average time/residue: 1.3994 time to fit residues: 205.7556 Evaluate side-chains 101 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 452 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 181 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 116 optimal weight: 0.0060 chunk 106 optimal weight: 2.9990 chunk 212 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 GLN B 486 HIS D 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.058145 restraints weight = 40978.773| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.04 r_work: 0.2630 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19184 Z= 0.126 Angle : 0.463 6.721 25996 Z= 0.246 Chirality : 0.043 0.152 2852 Planarity : 0.003 0.030 3336 Dihedral : 3.957 17.254 2504 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.11 % Allowed : 10.43 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2300 helix: 1.21 (0.19), residues: 796 sheet: 0.02 (0.33), residues: 284 loop : 0.23 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 192 HIS 0.003 0.001 HIS C 588 PHE 0.019 0.001 PHE A 506 TYR 0.013 0.001 TYR B 471 ARG 0.004 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 672) hydrogen bonds : angle 4.13820 ( 1869) covalent geometry : bond 0.00291 (19184) covalent geometry : angle 0.46310 (25996) *********************** 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 133 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8870 (mp10) cc_final: 0.8171 (mp10) REVERT: A 159 GLU cc_start: 0.9210 (mp0) cc_final: 0.8987 (mp0) REVERT: A 430 CYS cc_start: 0.9008 (m) cc_final: 0.8441 (m) REVERT: A 465 MET cc_start: 0.9598 (mtm) cc_final: 0.9190 (mtm) REVERT: A 473 MET cc_start: 0.9393 (mmm) cc_final: 0.9172 (mmm) REVERT: A 526 ASP cc_start: 0.8895 (t70) cc_final: 0.8458 (p0) REVERT: A 557 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8342 (mp0) REVERT: B 159 GLU cc_start: 0.9160 (mp0) cc_final: 0.8941 (pm20) REVERT: B 401 ASP cc_start: 0.8859 (m-30) cc_final: 0.8428 (p0) REVERT: B 465 MET cc_start: 0.9571 (mtm) cc_final: 0.9365 (mtm) REVERT: B 526 ASP cc_start: 0.8486 (t70) cc_final: 0.8007 (t0) REVERT: C 82 GLU cc_start: 0.7651 (pm20) cc_final: 0.7319 (pm20) REVERT: C 198 MET cc_start: 0.9132 (ttt) cc_final: 0.8928 (tpt) REVERT: C 465 MET cc_start: 0.9591 (mtm) cc_final: 0.9314 (mtm) REVERT: D 83 MET cc_start: 0.7653 (mtm) cc_final: 0.7357 (mtm) REVERT: D 117 GLU cc_start: 0.8406 (pp20) cc_final: 0.8202 (pp20) REVERT: D 132 GLN cc_start: 0.8849 (mp10) cc_final: 0.8151 (mp10) REVERT: D 159 GLU cc_start: 0.9169 (mp0) cc_final: 0.8875 (mp0) REVERT: D 359 ASP cc_start: 0.9158 (m-30) cc_final: 0.8817 (m-30) REVERT: D 430 CYS cc_start: 0.9031 (m) cc_final: 0.8463 (m) REVERT: D 465 MET cc_start: 0.9622 (mtm) cc_final: 0.9228 (mtm) REVERT: D 473 MET cc_start: 0.9384 (mmm) cc_final: 0.9166 (mmm) REVERT: D 526 ASP cc_start: 0.8578 (p0) cc_final: 0.8315 (p0) REVERT: D 564 MET cc_start: 0.8409 (pmm) cc_final: 0.8100 (tmm) outliers start: 23 outliers final: 5 residues processed: 127 average time/residue: 1.4558 time to fit residues: 208.2786 Evaluate side-chains 98 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 407 ILE 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: 8.9990 chunk 123 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 98 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 153 optimal weight: 5.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN 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 = 0.073871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.056205 restraints weight = 41393.628| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.14 r_work: 0.2597 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19184 Z= 0.151 Angle : 0.468 6.467 25996 Z= 0.249 Chirality : 0.043 0.149 2852 Planarity : 0.003 0.033 3336 Dihedral : 3.936 17.390 2504 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2300 helix: 1.35 (0.19), residues: 796 sheet: -0.28 (0.32), residues: 304 loop : 0.32 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 344 HIS 0.004 0.001 HIS C 588 PHE 0.033 0.001 PHE C 506 TYR 0.014 0.001 TYR C 471 ARG 0.003 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 672) hydrogen bonds : angle 4.08301 ( 1869) covalent geometry : bond 0.00349 (19184) covalent geometry : angle 0.46808 (25996) *********************** 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: 25 poor density : 102 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7758 (mtm) cc_final: 0.7479 (mtm) REVERT: A 132 GLN cc_start: 0.8880 (mp10) cc_final: 0.8162 (mp10) REVERT: A 159 GLU cc_start: 0.9247 (mp0) cc_final: 0.9013 (mp0) REVERT: A 198 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8622 (ttt) REVERT: A 203 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: A 430 CYS cc_start: 0.9050 (m) cc_final: 0.8528 (m) REVERT: A 465 MET cc_start: 0.9630 (mtm) cc_final: 0.9222 (mtm) REVERT: A 473 MET cc_start: 0.9413 (mmm) cc_final: 0.9182 (mmm) REVERT: A 526 ASP cc_start: 0.8945 (t70) cc_final: 0.8469 (p0) REVERT: A 557 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8362 (mp0) REVERT: A 564 MET cc_start: 0.8628 (pmm) cc_final: 0.8365 (tmm) REVERT: B 401 ASP cc_start: 0.8814 (m-30) cc_final: 0.8464 (p0) REVERT: B 465 MET cc_start: 0.9541 (mtm) cc_final: 0.9327 (mtm) REVERT: B 526 ASP cc_start: 0.8524 (t70) cc_final: 0.8020 (t0) REVERT: C 82 GLU cc_start: 0.7694 (pm20) cc_final: 0.7490 (pm20) REVERT: C 253 ILE cc_start: 0.9458 (mt) cc_final: 0.9171 (mm) REVERT: C 465 MET cc_start: 0.9581 (mtm) cc_final: 0.9292 (mtm) REVERT: D 83 MET cc_start: 0.7735 (mtm) cc_final: 0.7332 (mtm) REVERT: D 117 GLU cc_start: 0.8493 (pp20) cc_final: 0.8283 (pp20) REVERT: D 132 GLN cc_start: 0.8878 (mp10) cc_final: 0.8162 (mp10) REVERT: D 198 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8585 (ttt) REVERT: D 245 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: D 355 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8491 (tppp) REVERT: D 359 ASP cc_start: 0.9176 (m-30) cc_final: 0.8799 (m-30) REVERT: D 430 CYS cc_start: 0.9085 (m) cc_final: 0.8558 (m) REVERT: D 465 MET cc_start: 0.9645 (mtm) cc_final: 0.9279 (mtm) REVERT: D 473 MET cc_start: 0.9412 (mmm) cc_final: 0.9191 (mmm) REVERT: D 526 ASP cc_start: 0.8589 (p0) cc_final: 0.8312 (p0) outliers start: 25 outliers final: 7 residues processed: 118 average time/residue: 1.4629 time to fit residues: 194.0742 Evaluate side-chains 104 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 407 ILE 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 196 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 177 optimal weight: 9.9990 chunk 184 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057861 restraints weight = 41064.127| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.16 r_work: 0.2643 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 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 = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19184 Z= 0.097 Angle : 0.448 7.883 25996 Z= 0.237 Chirality : 0.042 0.147 2852 Planarity : 0.003 0.032 3336 Dihedral : 3.774 17.627 2504 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.67 % Allowed : 11.88 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2300 helix: 1.45 (0.19), residues: 796 sheet: -0.04 (0.33), residues: 284 loop : 0.32 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.003 0.001 HIS B 588 PHE 0.029 0.001 PHE B 506 TYR 0.012 0.001 TYR C 471 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.02670 ( 672) hydrogen bonds : angle 3.96119 ( 1869) covalent geometry : bond 0.00223 (19184) covalent geometry : angle 0.44762 (25996) *********************** 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 125 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7777 (mtm) cc_final: 0.7304 (mtm) REVERT: A 132 GLN cc_start: 0.8866 (mp10) cc_final: 0.8140 (mp10) REVERT: A 159 GLU cc_start: 0.9243 (mp0) cc_final: 0.9009 (mp0) REVERT: A 198 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8516 (ttt) REVERT: A 203 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8217 (mmm) REVERT: A 401 ASP cc_start: 0.8477 (t0) cc_final: 0.8114 (p0) REVERT: A 430 CYS cc_start: 0.8970 (m) cc_final: 0.8447 (m) REVERT: A 465 MET cc_start: 0.9613 (mtm) cc_final: 0.9250 (mtm) REVERT: A 473 MET cc_start: 0.9384 (mmm) cc_final: 0.9153 (mmm) REVERT: A 526 ASP cc_start: 0.8946 (t70) cc_final: 0.8444 (p0) REVERT: A 557 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8368 (mp0) REVERT: B 81 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7661 (mmm160) REVERT: B 401 ASP cc_start: 0.8784 (m-30) cc_final: 0.8458 (p0) REVERT: B 465 MET cc_start: 0.9541 (mtm) cc_final: 0.9232 (mtm) REVERT: B 506 PHE cc_start: 0.8728 (t80) cc_final: 0.8412 (t80) REVERT: B 526 ASP cc_start: 0.8553 (t70) cc_final: 0.8039 (t0) REVERT: D 0 HIS cc_start: 0.8487 (m-70) cc_final: 0.8209 (m-70) REVERT: D 83 MET cc_start: 0.7816 (mtm) cc_final: 0.7367 (mtm) REVERT: D 117 GLU cc_start: 0.8500 (pp20) cc_final: 0.8235 (pp20) REVERT: D 132 GLN cc_start: 0.8864 (mp10) cc_final: 0.8131 (mp10) REVERT: D 198 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8523 (ttt) REVERT: D 203 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8206 (mmm) REVERT: D 355 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8423 (tppp) REVERT: D 359 ASP cc_start: 0.9164 (m-30) cc_final: 0.8767 (m-30) REVERT: D 430 CYS cc_start: 0.9016 (m) cc_final: 0.8484 (m) REVERT: D 465 MET cc_start: 0.9616 (mtm) cc_final: 0.9276 (mtm) REVERT: D 473 MET cc_start: 0.9393 (mmm) cc_final: 0.9173 (mmm) REVERT: D 526 ASP cc_start: 0.8551 (p0) cc_final: 0.8220 (p0) REVERT: D 557 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8332 (mp0) REVERT: D 564 MET cc_start: 0.8330 (pmm) cc_final: 0.8008 (tmm) outliers start: 14 outliers final: 2 residues processed: 118 average time/residue: 1.4927 time to fit residues: 197.6690 Evaluate side-chains 104 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 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 90 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 196 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.058032 restraints weight = 40544.354| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.14 r_work: 0.2649 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 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 = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2625 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= 0.098 Angle : 0.442 8.952 25996 Z= 0.234 Chirality : 0.042 0.147 2852 Planarity : 0.003 0.034 3336 Dihedral : 3.703 17.292 2504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.91 % Allowed : 11.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2300 helix: 1.54 (0.19), residues: 796 sheet: 0.04 (0.33), residues: 284 loop : 0.35 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 316 HIS 0.002 0.001 HIS B 588 PHE 0.027 0.001 PHE B 506 TYR 0.010 0.001 TYR D 223 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 672) hydrogen bonds : angle 3.91222 ( 1869) covalent geometry : bond 0.00224 (19184) covalent geometry : angle 0.44241 (25996) *********************** 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 124 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7798 (mtm) cc_final: 0.7504 (mtm) REVERT: A 132 GLN cc_start: 0.8834 (mp10) cc_final: 0.8115 (mp10) REVERT: A 159 GLU cc_start: 0.9242 (mp0) cc_final: 0.9013 (mp0) REVERT: A 198 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8326 (ttt) REVERT: A 203 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8235 (mmm) REVERT: A 401 ASP cc_start: 0.8448 (t0) cc_final: 0.8216 (t0) REVERT: A 430 CYS cc_start: 0.8929 (m) cc_final: 0.8462 (m) REVERT: A 437 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: A 465 MET cc_start: 0.9609 (mtm) cc_final: 0.9245 (mtm) REVERT: A 473 MET cc_start: 0.9387 (mmm) cc_final: 0.9153 (mmm) REVERT: A 526 ASP cc_start: 0.8926 (t70) cc_final: 0.8400 (p0) REVERT: A 557 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8367 (mp0) REVERT: A 564 MET cc_start: 0.8605 (pmm) cc_final: 0.8326 (tmm) REVERT: B 401 ASP cc_start: 0.8817 (m-30) cc_final: 0.8459 (p0) REVERT: B 451 GLU cc_start: 0.9145 (tt0) cc_final: 0.8790 (tm-30) REVERT: B 465 MET cc_start: 0.9538 (mtm) cc_final: 0.9226 (mtm) REVERT: B 526 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8004 (t0) REVERT: C 82 GLU cc_start: 0.7574 (pm20) cc_final: 0.7289 (pm20) REVERT: C 253 ILE cc_start: 0.9384 (mt) cc_final: 0.9134 (mm) REVERT: C 465 MET cc_start: 0.9310 (mtp) cc_final: 0.9033 (mtp) REVERT: D 0 HIS cc_start: 0.8505 (m-70) cc_final: 0.8198 (m-70) REVERT: D 83 MET cc_start: 0.7758 (mtm) cc_final: 0.7472 (mtm) REVERT: D 117 GLU cc_start: 0.8567 (pp20) cc_final: 0.8307 (pp20) REVERT: D 132 GLN cc_start: 0.8890 (mp10) cc_final: 0.8176 (mp10) REVERT: D 198 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8491 (ttt) REVERT: D 203 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8218 (mmm) REVERT: D 355 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8427 (tppp) REVERT: D 359 ASP cc_start: 0.9159 (m-30) cc_final: 0.8761 (m-30) REVERT: D 430 CYS cc_start: 0.8959 (m) cc_final: 0.8479 (m) REVERT: D 465 MET cc_start: 0.9600 (mtm) cc_final: 0.9319 (mtm) REVERT: D 473 MET cc_start: 0.9372 (mmm) cc_final: 0.9150 (mmm) REVERT: D 526 ASP cc_start: 0.8539 (p0) cc_final: 0.8209 (p0) REVERT: D 557 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8317 (mp0) REVERT: D 564 MET cc_start: 0.8378 (pmm) cc_final: 0.8016 (tmm) outliers start: 19 outliers final: 5 residues processed: 117 average time/residue: 1.4766 time to fit residues: 195.2897 Evaluate side-chains 115 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 A residue 539 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 407 ILE 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 162 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 187 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- 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 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.054206 restraints weight = 41902.433| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.17 r_work: 0.2546 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 19184 Z= 0.247 Angle : 0.539 9.908 25996 Z= 0.286 Chirality : 0.046 0.170 2852 Planarity : 0.003 0.035 3336 Dihedral : 4.151 18.082 2504 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.06 % Allowed : 11.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2300 helix: 1.42 (0.19), residues: 796 sheet: -0.40 (0.31), residues: 304 loop : 0.32 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 113 HIS 0.005 0.001 HIS C 588 PHE 0.035 0.001 PHE C 506 TYR 0.033 0.002 TYR C 471 ARG 0.009 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 672) hydrogen bonds : angle 4.23780 ( 1869) covalent geometry : bond 0.00567 (19184) covalent geometry : angle 0.53930 (25996) *********************** 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: 22 poor density : 91 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7915 (mtm) cc_final: 0.7473 (mtm) REVERT: A 132 GLN cc_start: 0.8860 (mp10) cc_final: 0.8170 (mp10) REVERT: A 159 GLU cc_start: 0.9279 (mp0) cc_final: 0.9054 (mp0) REVERT: A 198 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8691 (ttt) REVERT: A 401 ASP cc_start: 0.8565 (t0) cc_final: 0.8296 (t0) REVERT: A 430 CYS cc_start: 0.9119 (m) cc_final: 0.8657 (m) REVERT: A 437 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: A 465 MET cc_start: 0.9637 (mtm) cc_final: 0.9283 (mtm) REVERT: A 473 MET cc_start: 0.9412 (mmm) cc_final: 0.9174 (mmm) REVERT: A 526 ASP cc_start: 0.9001 (t70) cc_final: 0.8397 (p0) REVERT: A 564 MET cc_start: 0.8569 (pmm) cc_final: 0.8263 (tmm) REVERT: B 401 ASP cc_start: 0.8919 (m-30) cc_final: 0.8612 (p0) REVERT: B 526 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8300 (t0) REVERT: C 82 GLU cc_start: 0.8002 (pm20) cc_final: 0.7633 (pm20) REVERT: C 253 ILE cc_start: 0.9395 (mt) cc_final: 0.9148 (mm) REVERT: D 83 MET cc_start: 0.7805 (mtm) cc_final: 0.7362 (mtm) REVERT: D 117 GLU cc_start: 0.8696 (pp20) cc_final: 0.8415 (pp20) REVERT: D 132 GLN cc_start: 0.8882 (mp10) cc_final: 0.8191 (mp10) REVERT: D 198 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8622 (ttt) REVERT: D 355 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8445 (tppp) REVERT: D 359 ASP cc_start: 0.9185 (m-30) cc_final: 0.8790 (m-30) REVERT: D 430 CYS cc_start: 0.9112 (m) cc_final: 0.8629 (m) REVERT: D 473 MET cc_start: 0.9388 (mmm) cc_final: 0.9162 (mmm) REVERT: D 526 ASP cc_start: 0.8636 (p0) cc_final: 0.8419 (p0) REVERT: D 564 MET cc_start: 0.8415 (pmm) cc_final: 0.8067 (tmm) outliers start: 22 outliers final: 3 residues processed: 108 average time/residue: 1.9084 time to fit residues: 233.3181 Evaluate side-chains 97 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET 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 100 optimal weight: 0.3980 chunk 136 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.058428 restraints weight = 40916.557| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.07 r_work: 0.2634 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19184 Z= 0.098 Angle : 0.461 8.820 25996 Z= 0.244 Chirality : 0.042 0.154 2852 Planarity : 0.003 0.049 3336 Dihedral : 3.841 18.173 2504 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.38 % Allowed : 12.74 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2300 helix: 1.54 (0.19), residues: 796 sheet: -0.33 (0.31), residues: 304 loop : 0.39 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 183 HIS 0.002 0.001 HIS B 588 PHE 0.017 0.001 PHE B 506 TYR 0.019 0.001 TYR C 471 ARG 0.012 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.02674 ( 672) hydrogen bonds : angle 4.00770 ( 1869) covalent geometry : bond 0.00226 (19184) covalent geometry : angle 0.46120 (25996) *********************** 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 110 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7922 (mtm) cc_final: 0.7571 (mtt) REVERT: A 132 GLN cc_start: 0.8887 (mp10) cc_final: 0.8195 (mp10) REVERT: A 159 GLU cc_start: 0.9264 (mp0) cc_final: 0.9049 (mp0) REVERT: A 198 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8304 (ttt) REVERT: A 401 ASP cc_start: 0.8466 (t0) cc_final: 0.8227 (t0) REVERT: A 430 CYS cc_start: 0.9002 (m) cc_final: 0.8468 (m) REVERT: A 465 MET cc_start: 0.9594 (mtm) cc_final: 0.9273 (mtm) REVERT: A 473 MET cc_start: 0.9388 (mmm) cc_final: 0.9161 (mmm) REVERT: A 526 ASP cc_start: 0.8918 (t70) cc_final: 0.8355 (p0) REVERT: A 557 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8372 (mp0) REVERT: A 564 MET cc_start: 0.8565 (pmm) cc_final: 0.8241 (tmm) REVERT: B 401 ASP cc_start: 0.8774 (m-30) cc_final: 0.8436 (p0) REVERT: B 506 PHE cc_start: 0.8787 (t80) cc_final: 0.8582 (t80) REVERT: B 526 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8178 (t0) REVERT: B 564 MET cc_start: 0.8850 (mpm) cc_final: 0.8650 (tmt) REVERT: C 82 GLU cc_start: 0.7703 (pm20) cc_final: 0.7406 (pm20) REVERT: C 253 ILE cc_start: 0.9395 (mt) cc_final: 0.9177 (mp) REVERT: D 83 MET cc_start: 0.7783 (mtm) cc_final: 0.7404 (mtm) REVERT: D 117 GLU cc_start: 0.8677 (pp20) cc_final: 0.8395 (pp20) REVERT: D 132 GLN cc_start: 0.8848 (mp10) cc_final: 0.8156 (mp10) REVERT: D 198 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8509 (ttt) REVERT: D 355 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8400 (tppp) REVERT: D 359 ASP cc_start: 0.9146 (m-30) cc_final: 0.8730 (m-30) REVERT: D 430 CYS cc_start: 0.9017 (m) cc_final: 0.8464 (m) REVERT: D 473 MET cc_start: 0.9339 (mmm) cc_final: 0.9117 (mmm) REVERT: D 526 ASP cc_start: 0.8541 (p0) cc_final: 0.8247 (p0) REVERT: D 557 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8368 (mp0) REVERT: D 564 MET cc_start: 0.8357 (pmm) cc_final: 0.7997 (tmm) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 1.4767 time to fit residues: 177.7488 Evaluate side-chains 102 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET 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 164 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** C 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.056375 restraints weight = 40690.642| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.12 r_work: 0.2598 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19184 Z= 0.152 Angle : 0.491 10.516 25996 Z= 0.259 Chirality : 0.043 0.150 2852 Planarity : 0.003 0.073 3336 Dihedral : 3.934 18.036 2504 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.38 % Allowed : 12.60 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2300 helix: 1.53 (0.19), residues: 796 sheet: -0.33 (0.32), residues: 304 loop : 0.41 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 344 HIS 0.003 0.001 HIS B 588 PHE 0.019 0.001 PHE A 506 TYR 0.012 0.001 TYR D 223 ARG 0.017 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 672) hydrogen bonds : angle 4.02771 ( 1869) covalent geometry : bond 0.00353 (19184) covalent geometry : angle 0.49064 (25996) ********************** 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 104 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 2.470 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7880 (mtm) cc_final: 0.7386 (mtm) REVERT: A 132 GLN cc_start: 0.8865 (mp10) cc_final: 0.8164 (mp10) REVERT: A 159 GLU cc_start: 0.9282 (mp0) cc_final: 0.9072 (mp0) REVERT: A 198 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8642 (ttt) REVERT: A 401 ASP cc_start: 0.8480 (t0) cc_final: 0.8241 (t0) REVERT: A 430 CYS cc_start: 0.9043 (m) cc_final: 0.8543 (m) REVERT: A 437 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 465 MET cc_start: 0.9608 (mtm) cc_final: 0.9265 (mtm) REVERT: A 473 MET cc_start: 0.9390 (mmm) cc_final: 0.9159 (mmm) REVERT: A 526 ASP cc_start: 0.8935 (t70) cc_final: 0.8355 (p0) REVERT: B 401 ASP cc_start: 0.8810 (m-30) cc_final: 0.8480 (p0) REVERT: B 526 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8247 (t0) REVERT: B 564 MET cc_start: 0.8870 (mpm) cc_final: 0.8653 (tmt) REVERT: C 82 GLU cc_start: 0.7742 (pm20) cc_final: 0.7436 (pm20) REVERT: C 253 ILE cc_start: 0.9393 (mt) cc_final: 0.9136 (mm) REVERT: D 83 MET cc_start: 0.7681 (mtm) cc_final: 0.7436 (mtm) REVERT: D 117 GLU cc_start: 0.8702 (pp20) cc_final: 0.8414 (pp20) REVERT: D 132 GLN cc_start: 0.8842 (mp10) cc_final: 0.8148 (mp10) REVERT: D 198 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8549 (ttt) REVERT: D 355 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8443 (tppp) REVERT: D 359 ASP cc_start: 0.9167 (m-30) cc_final: 0.8753 (m-30) REVERT: D 430 CYS cc_start: 0.9036 (m) cc_final: 0.8532 (m) REVERT: D 473 MET cc_start: 0.9339 (mmm) cc_final: 0.9110 (mmm) REVERT: D 526 ASP cc_start: 0.8570 (p0) cc_final: 0.8259 (p0) REVERT: D 557 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8359 (mp0) REVERT: D 564 MET cc_start: 0.8389 (pmm) cc_final: 0.8053 (tmm) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 1.6106 time to fit residues: 181.1310 Evaluate side-chains 101 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 198 MET 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 0 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.055166 restraints weight = 41671.399| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.16 r_work: 0.2574 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 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 = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19184 Z= 0.194 Angle : 0.518 9.754 25996 Z= 0.273 Chirality : 0.044 0.152 2852 Planarity : 0.003 0.073 3336 Dihedral : 4.079 18.392 2504 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.53 % Allowed : 12.60 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2300 helix: 1.48 (0.19), residues: 796 sheet: -0.38 (0.31), residues: 304 loop : 0.40 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 113 HIS 0.004 0.001 HIS B 588 PHE 0.029 0.001 PHE B 506 TYR 0.035 0.001 TYR C 471 ARG 0.018 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 672) hydrogen bonds : angle 4.12815 ( 1869) covalent geometry : bond 0.00449 (19184) covalent geometry : angle 0.51751 (25996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9487.84 seconds wall clock time: 164 minutes 36.08 seconds (9876.08 seconds total)