Starting phenix.real_space_refine on Fri Aug 7 20:26:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqy_65281/08_2026/9vqy_65281.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 120 5.16 5 Na 5 4.78 5 C 15012 2.51 5 N 3836 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23141 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5681 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 24, 'TRANS': 669} Chain breaks: 4 Chain: "B" Number of atoms: 5681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5681 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 24, 'TRANS': 669} Chain breaks: 4 Chain: "C" Number of atoms: 5681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5681 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 24, 'TRANS': 669} Chain breaks: 4 Chain: "D" Number of atoms: 5681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5681 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 24, 'TRANS': 669} Chain breaks: 4 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 106 Unusual residues: {' CA': 2, ' NA': 5, ' ZN': 1, 'CAM': 1, 'POV': 1, 'YZY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {' CA': 2, ' ZN': 1, 'CAM': 1, 'POV': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {' CA': 2, ' ZN': 1, 'CAM': 1, 'POV': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {' CA': 2, ' ZN': 1, 'CAM': 1, 'POV': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1195 SG CYS A 166 84.023 104.660 64.088 1.00122.63 S ATOM 1228 SG CYS A 171 80.929 104.375 61.808 1.00116.24 S ATOM 6876 SG CYS B 166 104.670 44.504 64.073 1.00122.63 S ATOM 6909 SG CYS B 171 104.386 47.600 61.796 1.00116.24 S ATOM 12557 SG CYS C 166 44.507 23.873 64.070 1.00122.63 S ATOM 12590 SG CYS C 171 47.603 24.157 61.793 1.00116.24 S ATOM 18238 SG CYS D 166 23.873 84.037 64.072 1.00122.63 S ATOM 18271 SG CYS D 171 24.158 80.941 61.794 1.00116.24 S Time building chain proxies: 4.84, per 1000 atoms: 0.21 Number of scatterers: 23141 At special positions: 0 Unit cell: (129.368, 129.368, 143.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 120 16.00 P 4 15.00 Na 5 11.00 O 4152 8.00 N 3836 7.00 C 15012 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: 1.79 Conformation dependent library (CDL) restraints added in 865.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" ND1 HIS A 162 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 166 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 171 " pdb=" ZN B1203 " pdb="ZN ZN B1203 " - pdb=" SG CYS B 166 " pdb="ZN ZN B1203 " - pdb=" ND1 HIS B 162 " pdb="ZN ZN B1203 " - pdb=" SG CYS B 171 " pdb=" ZN C1203 " pdb="ZN ZN C1203 " - pdb=" SG CYS C 166 " pdb="ZN ZN C1203 " - pdb=" ND1 HIS C 162 " pdb="ZN ZN C1203 " - pdb=" SG CYS C 171 " pdb=" ZN D1203 " pdb="ZN ZN D1203 " - pdb=" ND1 HIS D 162 " pdb="ZN ZN D1203 " - pdb=" SG CYS D 166 " pdb="ZN ZN D1203 " - pdb=" SG CYS D 171 " 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.533A pdb=" N GLU A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 14 " --> pdb=" O HIS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.679A pdb=" N ASP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.567A pdb=" N HIS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.531A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.552A pdb=" N ASP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 205 through 224 Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.631A pdb=" N TYR A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.951A pdb=" N MET A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 351 through 371 Processing helix chain 'A' and resid 408 through 432 Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 440 through 474 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.540A pdb=" N TRP A 485 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 506 Processing helix chain 'A' and resid 507 through 513 removed outlier: 4.187A pdb=" N TYR A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 529 through 556 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.505A pdb=" N GLU A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 622 through 642 Processing helix chain 'A' and resid 643 through 660 Processing helix chain 'A' and resid 662 through 677 removed outlier: 3.538A pdb=" N SER A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.799A pdb=" N ASN A 690 " --> pdb=" O PRO A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 759 Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.691A pdb=" N VAL A 767 " --> pdb=" O THR A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.533A pdb=" N GLU B 13 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 14 " --> pdb=" O HIS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.678A pdb=" N ASP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.567A pdb=" N HIS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.531A pdb=" N ASN B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.552A pdb=" N ASP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 227 through 248 removed outlier: 3.631A pdb=" N TYR B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.951A pdb=" N MET B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 351 through 371 Processing helix chain 'B' and resid 408 through 432 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 440 through 474 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.540A pdb=" N TRP B 485 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 506 Processing helix chain 'B' and resid 507 through 513 removed outlier: 4.186A pdb=" N TYR B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 529 through 556 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 606 through 608 No H-bonds generated for 'chain 'B' and resid 606 through 608' Processing helix chain 'B' and resid 613 through 618 removed outlier: 3.504A pdb=" N GLU B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 618' Processing helix chain 'B' and resid 622 through 642 Processing helix chain 'B' and resid 643 through 660 Processing helix chain 'B' and resid 662 through 677 removed outlier: 3.538A pdb=" N SER B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 690 removed outlier: 3.799A pdb=" N ASN B 690 " --> pdb=" O PRO B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 759 Processing helix chain 'B' and resid 763 through 789 removed outlier: 3.691A pdb=" N VAL B 767 " --> pdb=" O THR B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 removed outlier: 3.534A pdb=" N GLU C 13 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 14 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 31 Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.679A pdb=" N ASP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.567A pdb=" N HIS C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.531A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 144 through 154 Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.552A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 205 through 224 Processing helix chain 'C' and resid 227 through 248 removed outlier: 3.631A pdb=" N TYR C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 276 through 285 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.951A pdb=" N MET C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 351 through 371 Processing helix chain 'C' and resid 408 through 432 Processing helix chain 'C' and resid 436 through 439 Processing helix chain 'C' and resid 440 through 474 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.540A pdb=" N TRP C 485 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 506 Processing helix chain 'C' and resid 507 through 513 removed outlier: 4.187A pdb=" N TYR C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 516 No H-bonds generated for 'chain 'C' and resid 514 through 516' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 529 through 556 Processing helix chain 'C' and resid 557 through 564 Processing helix chain 'C' and resid 595 through 605 Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 613 through 618 removed outlier: 3.505A pdb=" N GLU C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 618 " --> pdb=" O ASP C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 613 through 618' Processing helix chain 'C' and resid 622 through 642 Processing helix chain 'C' and resid 643 through 660 Processing helix chain 'C' and resid 662 through 677 removed outlier: 3.538A pdb=" N SER C 677 " --> pdb=" O LYS C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 removed outlier: 3.798A pdb=" N ASN C 690 " --> pdb=" O PRO C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 759 Processing helix chain 'C' and resid 763 through 789 removed outlier: 3.691A pdb=" N VAL C 767 " --> pdb=" O THR C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.533A pdb=" N GLU D 13 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 14 " --> pdb=" O HIS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.679A pdb=" N ASP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.567A pdb=" N HIS D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.532A pdb=" N ASN D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.551A pdb=" N ASP D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 227 through 248 removed outlier: 3.632A pdb=" N TYR D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.951A pdb=" N MET D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 Processing helix chain 'D' and resid 351 through 371 Processing helix chain 'D' and resid 408 through 432 Processing helix chain 'D' and resid 436 through 439 Processing helix chain 'D' and resid 440 through 474 Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.540A pdb=" N TRP D 485 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 506 Processing helix chain 'D' and resid 507 through 513 removed outlier: 4.186A pdb=" N TYR D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 516 No H-bonds generated for 'chain 'D' and resid 514 through 516' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 529 through 556 Processing helix chain 'D' and resid 557 through 564 Processing helix chain 'D' and resid 595 through 605 Processing helix chain 'D' and resid 606 through 608 No H-bonds generated for 'chain 'D' and resid 606 through 608' Processing helix chain 'D' and resid 613 through 618 removed outlier: 3.505A pdb=" N GLU D 617 " --> pdb=" O LEU D 613 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 613 through 618' Processing helix chain 'D' and resid 622 through 642 Processing helix chain 'D' and resid 643 through 660 Processing helix chain 'D' and resid 662 through 677 removed outlier: 3.538A pdb=" N SER D 677 " --> pdb=" O LYS D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 690 removed outlier: 3.798A pdb=" N ASN D 690 " --> pdb=" O PRO D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 759 Processing helix chain 'D' and resid 763 through 789 removed outlier: 3.691A pdb=" N VAL D 767 " --> pdb=" O THR D 763 " (cutoff:3.500A) 1500 hydrogen bonds defined for protein. 4452 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: 4.02 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3712 1.31 - 1.43: 6429 1.43 - 1.56: 13279 1.56 - 1.69: 8 1.69 - 1.81: 208 Bond restraints: 23636 Sorted by residual: bond pdb=" C20 YZY A1204 " pdb=" O4 YZY A1204 " ideal model delta sigma weight residual 1.328 1.399 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C20 YZY C1204 " pdb=" O4 YZY C1204 " ideal model delta sigma weight residual 1.328 1.399 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C20 YZY B1204 " pdb=" O4 YZY B1204 " ideal model delta sigma weight residual 1.328 1.399 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C20 YZY D1204 " pdb=" O4 YZY D1204 " ideal model delta sigma weight residual 1.328 1.398 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3 YZY C1204 " pdb=" O2 YZY C1204 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 23631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 31005 1.81 - 3.63: 717 3.63 - 5.44: 158 5.44 - 7.25: 44 7.25 - 9.06: 24 Bond angle restraints: 31948 Sorted by residual: angle pdb=" N ASP C 446 " pdb=" CA ASP C 446 " pdb=" C ASP C 446 " ideal model delta sigma weight residual 111.14 107.00 4.14 1.08e+00 8.57e-01 1.47e+01 angle pdb=" N ASP B 446 " pdb=" CA ASP B 446 " pdb=" C ASP B 446 " ideal model delta sigma weight residual 111.14 107.02 4.12 1.08e+00 8.57e-01 1.46e+01 angle pdb=" N ASP D 446 " pdb=" CA ASP D 446 " pdb=" C ASP D 446 " ideal model delta sigma weight residual 111.14 107.02 4.12 1.08e+00 8.57e-01 1.46e+01 angle pdb=" N ASP A 446 " pdb=" CA ASP A 446 " pdb=" C ASP A 446 " ideal model delta sigma weight residual 111.14 107.04 4.10 1.08e+00 8.57e-01 1.44e+01 angle pdb=" N TRP C 605 " pdb=" CA TRP C 605 " pdb=" C TRP C 605 " ideal model delta sigma weight residual 113.20 108.68 4.52 1.21e+00 6.83e-01 1.40e+01 ... (remaining 31943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 13652 28.14 - 56.27: 572 56.27 - 84.41: 68 84.41 - 112.54: 8 112.54 - 140.68: 4 Dihedral angle restraints: 14304 sinusoidal: 6116 harmonic: 8188 Sorted by residual: dihedral pdb=" C26 YZY B1204 " pdb=" C27 YZY B1204 " pdb=" C28 YZY B1204 " pdb=" C29 YZY B1204 " ideal model delta sinusoidal sigma weight residual 119.11 -100.21 -140.68 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C26 YZY D1204 " pdb=" C27 YZY D1204 " pdb=" C28 YZY D1204 " pdb=" C29 YZY D1204 " ideal model delta sinusoidal sigma weight residual 119.11 -100.23 -140.66 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C26 YZY A1204 " pdb=" C27 YZY A1204 " pdb=" C28 YZY A1204 " pdb=" C29 YZY A1204 " ideal model delta sinusoidal sigma weight residual 119.11 -100.24 -140.65 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 14301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2753 0.050 - 0.101: 685 0.101 - 0.151: 82 0.151 - 0.201: 12 0.201 - 0.252: 8 Chirality restraints: 3540 Sorted by residual: chirality pdb=" CA MET B 274 " pdb=" N MET B 274 " pdb=" C MET B 274 " pdb=" CB MET B 274 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA MET D 274 " pdb=" N MET D 274 " pdb=" C MET D 274 " pdb=" CB MET D 274 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA MET A 274 " pdb=" N MET A 274 " pdb=" C MET A 274 " pdb=" CB MET A 274 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3537 not shown) Planarity restraints: 4008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 55 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 56 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 55 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO D 56 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 55 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 56 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.031 5.00e-02 4.00e+02 ... (remaining 4005 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1022 2.73 - 3.27: 23596 3.27 - 3.81: 38629 3.81 - 4.36: 44450 4.36 - 4.90: 76875 Nonbonded interactions: 184572 Sorted by model distance: nonbonded pdb=" O LEU B 610 " pdb=" CD1 LEU B 610 " model vdw 2.183 3.460 nonbonded pdb=" O LEU D 610 " pdb=" CD1 LEU D 610 " model vdw 2.184 3.460 nonbonded pdb=" O LEU A 610 " pdb=" CD1 LEU A 610 " model vdw 2.184 3.460 nonbonded pdb=" O LEU C 610 " pdb=" CD1 LEU C 610 " model vdw 2.185 3.460 nonbonded pdb=" OD2 ASP A 532 " pdb=" OG SER A 655 " model vdw 2.253 3.040 ... (remaining 184567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 1206) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23648 Z= 0.206 Angle : 0.738 9.063 31948 Z= 0.387 Chirality : 0.044 0.252 3540 Planarity : 0.006 0.055 4008 Dihedral : 15.081 140.675 8960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2736 helix: 0.13 (0.11), residues: 2008 sheet: None (None), residues: 0 loop : -1.01 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.012 0.002 TYR B 511 PHE 0.026 0.002 PHE B 330 TRP 0.013 0.002 TRP D 304 HIS 0.003 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (23636) covalent geometry : angle 0.73805 / 0.39 (31948) hydrogen bonds : bond 0.13918 / 9.36 ( 1500) hydrogen bonds : angle 5.39240 / 3.89 ( 4452) metal coordination : bond 0.00100 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.894 Fit side-chains REVERT: A 437 TYR cc_start: 0.8603 (t80) cc_final: 0.8264 (t80) REVERT: A 534 MET cc_start: 0.7435 (ppp) cc_final: 0.7178 (ppp) REVERT: A 537 PHE cc_start: 0.8203 (m-10) cc_final: 0.7881 (m-80) REVERT: A 648 LEU cc_start: 0.9077 (tp) cc_final: 0.8773 (tt) REVERT: B 409 PHE cc_start: 0.8119 (t80) cc_final: 0.7909 (t80) REVERT: B 648 LEU cc_start: 0.9113 (tp) cc_final: 0.8799 (tt) REVERT: C 409 PHE cc_start: 0.8123 (t80) cc_final: 0.7912 (t80) REVERT: C 648 LEU cc_start: 0.9114 (tp) cc_final: 0.8801 (tt) REVERT: D 409 PHE cc_start: 0.8120 (t80) cc_final: 0.7910 (t80) REVERT: D 648 LEU cc_start: 0.9112 (tp) cc_final: 0.8797 (tt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1477 time to fit residues: 102.4437 Evaluate side-chains 336 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN B 12 GLN C 12 GLN D 12 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103569 restraints weight = 43754.718| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.78 r_work: 0.3257 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23648 Z= 0.125 Angle : 0.552 8.721 31948 Z= 0.279 Chirality : 0.039 0.225 3540 Planarity : 0.004 0.046 4008 Dihedral : 10.029 125.045 3420 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.32 % Allowed : 13.60 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2736 helix: 1.56 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -0.69 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 592 TYR 0.021 0.001 TYR C 511 PHE 0.021 0.001 PHE A 330 TRP 0.023 0.002 TRP C 485 HIS 0.003 0.001 HIS D 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23636) covalent geometry : angle 0.55244 / 0.28 (31948) hydrogen bonds : bond 0.03735 / 2.50 ( 1500) hydrogen bonds : angle 3.79990 / 2.73 ( 4452) metal coordination : bond 0.00099 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 431 time to evaluate : 0.730 Fit side-chains REVERT: A 437 TYR cc_start: 0.8670 (t80) cc_final: 0.8330 (t80) REVERT: A 480 LEU cc_start: 0.8248 (mp) cc_final: 0.7999 (mp) REVERT: A 533 ILE cc_start: 0.8700 (mt) cc_final: 0.7940 (mt) REVERT: A 534 MET cc_start: 0.7564 (ppp) cc_final: 0.7340 (ppp) REVERT: A 537 PHE cc_start: 0.8362 (m-10) cc_final: 0.8045 (m-80) REVERT: A 742 MET cc_start: 0.9110 (mmt) cc_final: 0.8693 (mmt) REVERT: B 480 LEU cc_start: 0.8217 (mp) cc_final: 0.7962 (mp) REVERT: B 533 ILE cc_start: 0.8734 (mt) cc_final: 0.7908 (mt) REVERT: B 534 MET cc_start: 0.7586 (ppp) cc_final: 0.7371 (ppp) REVERT: B 537 PHE cc_start: 0.8322 (m-10) cc_final: 0.8025 (m-80) REVERT: B 666 GLU cc_start: 0.8658 (tt0) cc_final: 0.8359 (mt-10) REVERT: B 742 MET cc_start: 0.9112 (mmt) cc_final: 0.8693 (mmt) REVERT: C 437 TYR cc_start: 0.8659 (t80) cc_final: 0.8345 (t80) REVERT: C 480 LEU cc_start: 0.8206 (mp) cc_final: 0.7937 (mp) REVERT: C 534 MET cc_start: 0.7542 (ppp) cc_final: 0.7301 (ppp) REVERT: C 537 PHE cc_start: 0.8234 (m-10) cc_final: 0.7926 (m-80) REVERT: C 666 GLU cc_start: 0.8650 (tt0) cc_final: 0.8344 (mt-10) REVERT: C 742 MET cc_start: 0.9113 (mmt) cc_final: 0.8692 (mmt) REVERT: D 437 TYR cc_start: 0.8663 (t80) cc_final: 0.8350 (t80) REVERT: D 480 LEU cc_start: 0.8200 (mp) cc_final: 0.7938 (mp) REVERT: D 533 ILE cc_start: 0.8719 (mt) cc_final: 0.7821 (mt) REVERT: D 534 MET cc_start: 0.7592 (ppp) cc_final: 0.7351 (ppp) REVERT: D 537 PHE cc_start: 0.8326 (m-10) cc_final: 0.7961 (m-80) REVERT: D 666 GLU cc_start: 0.8641 (tt0) cc_final: 0.8382 (mt-10) REVERT: D 742 MET cc_start: 0.9109 (mmt) cc_final: 0.8686 (mmt) outliers start: 33 outliers final: 18 residues processed: 455 average time/residue: 0.1359 time to fit residues: 101.6607 Evaluate side-chains 381 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 363 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 138 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 275 HIS B 12 GLN B 275 HIS C 12 GLN C 275 HIS D 12 GLN D 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100155 restraints weight = 43994.590| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.73 r_work: 0.3202 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23648 Z= 0.181 Angle : 0.592 8.444 31948 Z= 0.302 Chirality : 0.041 0.317 3540 Planarity : 0.004 0.045 4008 Dihedral : 9.808 106.306 3420 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.96 % Allowed : 14.08 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.16), residues: 2736 helix: 2.05 (0.11), residues: 2028 sheet: None (None), residues: 0 loop : -0.43 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 592 TYR 0.020 0.002 TYR A 511 PHE 0.025 0.002 PHE A 464 TRP 0.027 0.002 TRP A 485 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (23636) covalent geometry : angle 0.59160 / 0.30 (31948) hydrogen bonds : bond 0.03955 / 2.64 ( 1500) hydrogen bonds : angle 3.75952 / 2.70 ( 4452) metal coordination : bond 0.00136 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 ILE cc_start: 0.8808 (mt) cc_final: 0.8245 (mt) REVERT: A 537 PHE cc_start: 0.8514 (m-10) cc_final: 0.8254 (m-80) REVERT: A 742 MET cc_start: 0.9131 (mmt) cc_final: 0.8756 (mmt) REVERT: B 533 ILE cc_start: 0.8827 (mt) cc_final: 0.8200 (mt) REVERT: B 537 PHE cc_start: 0.8476 (m-10) cc_final: 0.8176 (m-80) REVERT: B 656 TYR cc_start: 0.8960 (t80) cc_final: 0.8704 (t80) REVERT: B 742 MET cc_start: 0.9139 (mmt) cc_final: 0.8764 (mmt) REVERT: C 446 ASP cc_start: 0.8836 (t0) cc_final: 0.8627 (t0) REVERT: C 537 PHE cc_start: 0.8482 (m-10) cc_final: 0.8160 (m-80) REVERT: C 656 TYR cc_start: 0.8967 (t80) cc_final: 0.8711 (t80) REVERT: C 742 MET cc_start: 0.9138 (mmt) cc_final: 0.8763 (mmt) REVERT: D 446 ASP cc_start: 0.8814 (t0) cc_final: 0.8607 (t0) REVERT: D 533 ILE cc_start: 0.8808 (mt) cc_final: 0.8204 (mt) REVERT: D 537 PHE cc_start: 0.8470 (m-10) cc_final: 0.8202 (m-80) REVERT: D 656 TYR cc_start: 0.8972 (t80) cc_final: 0.8716 (t80) REVERT: D 666 GLU cc_start: 0.8686 (tt0) cc_final: 0.8453 (mt-10) REVERT: D 742 MET cc_start: 0.9127 (mmt) cc_final: 0.8749 (mmt) outliers start: 49 outliers final: 27 residues processed: 424 average time/residue: 0.1466 time to fit residues: 101.4314 Evaluate side-chains 375 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 101 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 68 ASN A 646 ASN B 12 GLN B 68 ASN B 646 ASN C 12 GLN C 68 ASN C 646 ASN D 12 GLN D 68 ASN D 646 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102800 restraints weight = 43463.309| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.74 r_work: 0.3248 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23648 Z= 0.112 Angle : 0.525 8.233 31948 Z= 0.266 Chirality : 0.038 0.141 3540 Planarity : 0.004 0.045 4008 Dihedral : 9.273 89.505 3420 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 15.92 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.16), residues: 2736 helix: 2.33 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.30 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 592 TYR 0.017 0.001 TYR A 656 PHE 0.021 0.001 PHE B 330 TRP 0.030 0.002 TRP B 485 HIS 0.002 0.000 HIS C 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (23636) covalent geometry : angle 0.52452 / 0.27 (31948) hydrogen bonds : bond 0.03420 / 2.29 ( 1500) hydrogen bonds : angle 3.54455 / 2.54 ( 4452) metal coordination : bond 0.00072 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 397 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TYR cc_start: 0.8694 (t80) cc_final: 0.8296 (t80) REVERT: A 533 ILE cc_start: 0.8749 (mt) cc_final: 0.8303 (mt) REVERT: A 537 PHE cc_start: 0.8586 (m-10) cc_final: 0.8326 (m-80) REVERT: A 648 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8461 (tp) REVERT: A 742 MET cc_start: 0.9131 (mmt) cc_final: 0.8710 (mmt) REVERT: B 421 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9189 (mp) REVERT: B 446 ASP cc_start: 0.8781 (t0) cc_final: 0.8577 (t0) REVERT: B 533 ILE cc_start: 0.8790 (mt) cc_final: 0.8336 (mt) REVERT: B 537 PHE cc_start: 0.8546 (m-10) cc_final: 0.8313 (m-80) REVERT: B 648 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 656 TYR cc_start: 0.8924 (t80) cc_final: 0.8648 (t80) REVERT: B 742 MET cc_start: 0.9127 (mmt) cc_final: 0.8702 (mmt) REVERT: C 446 ASP cc_start: 0.8747 (t0) cc_final: 0.8545 (t0) REVERT: C 537 PHE cc_start: 0.8525 (m-10) cc_final: 0.8268 (m-80) REVERT: C 656 TYR cc_start: 0.8937 (t80) cc_final: 0.8640 (t80) REVERT: C 742 MET cc_start: 0.9127 (mmt) cc_final: 0.8699 (mmt) REVERT: D 446 ASP cc_start: 0.8781 (t0) cc_final: 0.8575 (t0) REVERT: D 533 ILE cc_start: 0.8773 (mt) cc_final: 0.8311 (mt) REVERT: D 537 PHE cc_start: 0.8521 (m-10) cc_final: 0.8309 (m-80) REVERT: D 648 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8489 (tt) REVERT: D 656 TYR cc_start: 0.8946 (t80) cc_final: 0.8661 (t80) REVERT: D 742 MET cc_start: 0.9141 (mmt) cc_final: 0.8718 (mmt) outliers start: 54 outliers final: 26 residues processed: 430 average time/residue: 0.1352 time to fit residues: 97.9051 Evaluate side-chains 394 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 364 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 174 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 68 ASN B 12 GLN B 68 ASN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 68 ASN D 12 GLN D 68 ASN ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101286 restraints weight = 43386.341| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.72 r_work: 0.3218 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23648 Z= 0.148 Angle : 0.558 7.663 31948 Z= 0.281 Chirality : 0.040 0.288 3540 Planarity : 0.004 0.045 4008 Dihedral : 9.140 86.956 3420 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.44 % Allowed : 16.68 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.16), residues: 2736 helix: 2.47 (0.11), residues: 2028 sheet: None (None), residues: 0 loop : -0.27 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 592 TYR 0.021 0.002 TYR A 511 PHE 0.022 0.001 PHE B 464 TRP 0.034 0.002 TRP A 485 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (23636) covalent geometry : angle 0.55780 / 0.28 (31948) hydrogen bonds : bond 0.03635 / 2.42 ( 1500) hydrogen bonds : angle 3.58010 / 2.57 ( 4452) metal coordination : bond 0.00118 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 400 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 437 TYR cc_start: 0.8695 (t80) cc_final: 0.8233 (t80) REVERT: A 533 ILE cc_start: 0.8752 (mt) cc_final: 0.8350 (mt) REVERT: A 537 PHE cc_start: 0.8630 (m-10) cc_final: 0.8394 (m-80) REVERT: A 742 MET cc_start: 0.9097 (mmt) cc_final: 0.8742 (mmt) REVERT: B 68 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.7969 (t0) REVERT: B 437 TYR cc_start: 0.8683 (t80) cc_final: 0.8235 (t80) REVERT: B 446 ASP cc_start: 0.8813 (t0) cc_final: 0.8607 (t0) REVERT: B 533 ILE cc_start: 0.8739 (mt) cc_final: 0.8326 (mt) REVERT: B 537 PHE cc_start: 0.8630 (m-10) cc_final: 0.8398 (m-80) REVERT: B 641 ILE cc_start: 0.9103 (mm) cc_final: 0.8782 (pt) REVERT: B 656 TYR cc_start: 0.8971 (t80) cc_final: 0.8690 (t80) REVERT: B 742 MET cc_start: 0.9112 (mmt) cc_final: 0.8762 (mmt) REVERT: C 68 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 226 GLU cc_start: 0.8729 (pm20) cc_final: 0.8509 (pm20) REVERT: C 437 TYR cc_start: 0.8676 (t80) cc_final: 0.8227 (t80) REVERT: C 537 PHE cc_start: 0.8579 (m-10) cc_final: 0.8289 (m-80) REVERT: C 641 ILE cc_start: 0.9079 (mm) cc_final: 0.8738 (pt) REVERT: C 656 TYR cc_start: 0.8956 (t80) cc_final: 0.8687 (t80) REVERT: C 742 MET cc_start: 0.9125 (mmt) cc_final: 0.8776 (mmt) REVERT: D 68 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8002 (t0) REVERT: D 437 TYR cc_start: 0.8686 (t80) cc_final: 0.8242 (t80) REVERT: D 446 ASP cc_start: 0.8804 (t0) cc_final: 0.8604 (t0) REVERT: D 533 ILE cc_start: 0.8742 (mt) cc_final: 0.8256 (mt) REVERT: D 537 PHE cc_start: 0.8556 (m-10) cc_final: 0.8322 (m-80) REVERT: D 641 ILE cc_start: 0.9100 (mm) cc_final: 0.8786 (pt) REVERT: D 656 TYR cc_start: 0.8957 (t80) cc_final: 0.8662 (t80) REVERT: D 742 MET cc_start: 0.9105 (mmt) cc_final: 0.8750 (mmt) outliers start: 61 outliers final: 35 residues processed: 436 average time/residue: 0.1392 time to fit residues: 100.0822 Evaluate side-chains 392 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 353 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 128 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 262 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 68 ASN B 12 GLN B 68 ASN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 68 ASN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104371 restraints weight = 43367.535| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.75 r_work: 0.3267 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23648 Z= 0.105 Angle : 0.537 8.352 31948 Z= 0.270 Chirality : 0.038 0.139 3540 Planarity : 0.004 0.045 4008 Dihedral : 8.718 84.159 3420 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.84 % Allowed : 17.92 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.16), residues: 2736 helix: 2.48 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 592 TYR 0.021 0.001 TYR A 636 PHE 0.021 0.001 PHE A 330 TRP 0.044 0.002 TRP B 485 HIS 0.002 0.000 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (23636) covalent geometry : angle 0.53673 / 0.27 (31948) hydrogen bonds : bond 0.03304 / 2.20 ( 1500) hydrogen bonds : angle 3.44615 / 2.48 ( 4452) metal coordination : bond 0.00050 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 372 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8266 (t0) REVERT: A 226 GLU cc_start: 0.8672 (pm20) cc_final: 0.8464 (pm20) REVERT: A 421 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9147 (mp) REVERT: A 437 TYR cc_start: 0.8662 (t80) cc_final: 0.8186 (t80) REVERT: A 533 ILE cc_start: 0.8707 (mt) cc_final: 0.8358 (mt) REVERT: A 537 PHE cc_start: 0.8626 (m-10) cc_final: 0.8393 (m-80) REVERT: A 742 MET cc_start: 0.9102 (mmt) cc_final: 0.8707 (mmt) REVERT: B 68 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (t0) REVERT: B 226 GLU cc_start: 0.8664 (pm20) cc_final: 0.8452 (pm20) REVERT: B 437 TYR cc_start: 0.8690 (t80) cc_final: 0.8260 (t80) REVERT: B 533 ILE cc_start: 0.8684 (mt) cc_final: 0.8328 (mt) REVERT: B 537 PHE cc_start: 0.8615 (m-10) cc_final: 0.8380 (m-80) REVERT: B 592 ARG cc_start: 0.7535 (tpt-90) cc_final: 0.7095 (tpt-90) REVERT: B 656 TYR cc_start: 0.8948 (t80) cc_final: 0.8641 (t80) REVERT: B 742 MET cc_start: 0.9108 (mmt) cc_final: 0.8714 (mmt) REVERT: C 68 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8280 (t0) REVERT: C 437 TYR cc_start: 0.8647 (t80) cc_final: 0.8230 (t80) REVERT: C 537 PHE cc_start: 0.8615 (m-10) cc_final: 0.8362 (m-80) REVERT: C 592 ARG cc_start: 0.7538 (tpt-90) cc_final: 0.7101 (tpt-90) REVERT: C 742 MET cc_start: 0.9119 (mmt) cc_final: 0.8730 (mmt) REVERT: D 68 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8279 (t0) REVERT: D 226 GLU cc_start: 0.8669 (pm20) cc_final: 0.8460 (pm20) REVERT: D 437 TYR cc_start: 0.8690 (t80) cc_final: 0.8267 (t80) REVERT: D 533 ILE cc_start: 0.8672 (mt) cc_final: 0.8250 (mt) REVERT: D 537 PHE cc_start: 0.8505 (m-10) cc_final: 0.8286 (m-80) REVERT: D 592 ARG cc_start: 0.7497 (tpt-90) cc_final: 0.7086 (tpt-90) REVERT: D 656 TYR cc_start: 0.8949 (t80) cc_final: 0.8647 (t80) REVERT: D 742 MET cc_start: 0.9096 (mmt) cc_final: 0.8704 (mmt) outliers start: 46 outliers final: 31 residues processed: 398 average time/residue: 0.1345 time to fit residues: 87.8154 Evaluate side-chains 380 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 69 optimal weight: 0.4980 chunk 248 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 256 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 68 ASN A 293 HIS B 12 GLN B 68 ASN B 293 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 68 ASN C 293 HIS ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 68 ASN D 293 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104519 restraints weight = 43245.704| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.75 r_work: 0.3266 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23648 Z= 0.108 Angle : 0.551 10.649 31948 Z= 0.276 Chirality : 0.038 0.144 3540 Planarity : 0.004 0.045 4008 Dihedral : 8.540 83.664 3420 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.76 % Allowed : 18.48 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.16), residues: 2736 helix: 2.52 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.17 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 592 TYR 0.033 0.002 TYR A 636 PHE 0.020 0.001 PHE B 330 TRP 0.047 0.002 TRP B 485 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23636) covalent geometry : angle 0.55101 / 0.28 (31948) hydrogen bonds : bond 0.03272 / 2.18 ( 1500) hydrogen bonds : angle 3.44776 / 2.48 ( 4452) metal coordination : bond 0.00046 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 367 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8203 (t0) REVERT: A 421 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9173 (mp) REVERT: A 533 ILE cc_start: 0.8640 (mt) cc_final: 0.8231 (mt) REVERT: A 537 PHE cc_start: 0.8613 (m-10) cc_final: 0.8385 (m-80) REVERT: A 656 TYR cc_start: 0.8928 (t80) cc_final: 0.8512 (t80) REVERT: A 742 MET cc_start: 0.9082 (mmt) cc_final: 0.8689 (mmt) REVERT: B 68 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8159 (t0) REVERT: B 437 TYR cc_start: 0.8658 (t80) cc_final: 0.8176 (t80) REVERT: B 533 ILE cc_start: 0.8613 (mt) cc_final: 0.8311 (mm) REVERT: B 537 PHE cc_start: 0.8616 (m-10) cc_final: 0.8406 (m-80) REVERT: B 592 ARG cc_start: 0.7749 (tpt-90) cc_final: 0.7437 (tpt-90) REVERT: B 656 TYR cc_start: 0.8964 (t80) cc_final: 0.8695 (t80) REVERT: B 742 MET cc_start: 0.9096 (mmt) cc_final: 0.8704 (mmt) REVERT: C 68 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8186 (t0) REVERT: C 437 TYR cc_start: 0.8650 (t80) cc_final: 0.8177 (t80) REVERT: C 537 PHE cc_start: 0.8597 (m-10) cc_final: 0.8333 (m-80) REVERT: C 641 ILE cc_start: 0.9105 (mm) cc_final: 0.8797 (pt) REVERT: C 742 MET cc_start: 0.9092 (mmt) cc_final: 0.8701 (mmt) REVERT: D 68 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8189 (t0) REVERT: D 437 TYR cc_start: 0.8665 (t80) cc_final: 0.8195 (t80) REVERT: D 533 ILE cc_start: 0.8625 (mt) cc_final: 0.8172 (mt) REVERT: D 656 TYR cc_start: 0.8930 (t80) cc_final: 0.8614 (t80) REVERT: D 742 MET cc_start: 0.9086 (mmt) cc_final: 0.8691 (mmt) outliers start: 44 outliers final: 31 residues processed: 399 average time/residue: 0.1384 time to fit residues: 90.1896 Evaluate side-chains 381 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 692 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 98 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 131 optimal weight: 0.0470 chunk 101 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104043 restraints weight = 42879.672| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.69 r_work: 0.3250 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23648 Z= 0.104 Angle : 0.553 11.138 31948 Z= 0.275 Chirality : 0.038 0.144 3540 Planarity : 0.004 0.045 4008 Dihedral : 8.237 83.513 3420 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.84 % Allowed : 17.56 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.16), residues: 2736 helix: 2.55 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.15 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 592 TYR 0.036 0.002 TYR B 636 PHE 0.028 0.001 PHE D 537 TRP 0.041 0.002 TRP A 485 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (23636) covalent geometry : angle 0.55321 / 0.28 (31948) hydrogen bonds : bond 0.03205 / 2.14 ( 1500) hydrogen bonds : angle 3.39595 / 2.44 ( 4452) metal coordination : bond 0.00036 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 377 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 421 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 533 ILE cc_start: 0.8607 (mt) cc_final: 0.8174 (mt) REVERT: A 537 PHE cc_start: 0.8711 (m-10) cc_final: 0.8452 (m-80) REVERT: A 742 MET cc_start: 0.9083 (mmt) cc_final: 0.8703 (mmt) REVERT: B 12 GLN cc_start: 0.8072 (pt0) cc_final: 0.7848 (pt0) REVERT: B 68 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8151 (t0) REVERT: B 421 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9124 (mp) REVERT: B 437 TYR cc_start: 0.8652 (t80) cc_final: 0.8101 (t80) REVERT: B 533 ILE cc_start: 0.8524 (mt) cc_final: 0.8259 (mm) REVERT: B 592 ARG cc_start: 0.7792 (tpt-90) cc_final: 0.7397 (tpt-90) REVERT: B 626 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7423 (mmm160) REVERT: B 656 TYR cc_start: 0.8938 (t80) cc_final: 0.8634 (t80) REVERT: B 742 MET cc_start: 0.9096 (mmt) cc_final: 0.8714 (mmt) REVERT: C 12 GLN cc_start: 0.8088 (pt0) cc_final: 0.7865 (pt0) REVERT: C 68 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (t0) REVERT: C 437 TYR cc_start: 0.8642 (t80) cc_final: 0.8110 (t80) REVERT: C 537 PHE cc_start: 0.8697 (m-10) cc_final: 0.8415 (m-80) REVERT: C 742 MET cc_start: 0.9115 (mmt) cc_final: 0.8744 (mmt) REVERT: D 12 GLN cc_start: 0.8088 (pt0) cc_final: 0.7866 (pt0) REVERT: D 68 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8200 (t0) REVERT: D 437 TYR cc_start: 0.8657 (t80) cc_final: 0.8122 (t80) REVERT: D 742 MET cc_start: 0.9090 (mmt) cc_final: 0.8712 (mmt) outliers start: 46 outliers final: 32 residues processed: 411 average time/residue: 0.1309 time to fit residues: 88.3958 Evaluate side-chains 383 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 739 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 78 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103226 restraints weight = 43290.599| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.70 r_work: 0.3241 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23648 Z= 0.115 Angle : 0.578 11.893 31948 Z= 0.285 Chirality : 0.038 0.135 3540 Planarity : 0.004 0.045 4008 Dihedral : 8.033 83.548 3420 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.48 % Allowed : 18.84 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.16), residues: 2736 helix: 2.54 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 592 TYR 0.051 0.002 TYR B 636 PHE 0.030 0.001 PHE B 537 TRP 0.037 0.002 TRP A 485 HIS 0.002 0.000 HIS C 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23636) covalent geometry : angle 0.57769 / 0.29 (31948) hydrogen bonds : bond 0.03292 / 2.19 ( 1500) hydrogen bonds : angle 3.44965 / 2.48 ( 4452) metal coordination : bond 0.00061 / 0.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 366 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 421 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9145 (mp) REVERT: A 533 ILE cc_start: 0.8588 (mt) cc_final: 0.8083 (mt) REVERT: A 537 PHE cc_start: 0.8702 (m-10) cc_final: 0.8376 (m-80) REVERT: A 742 MET cc_start: 0.9100 (mmt) cc_final: 0.8723 (mmt) REVERT: A 772 GLN cc_start: 0.7995 (tp40) cc_final: 0.7019 (tm-30) REVERT: B 12 GLN cc_start: 0.8078 (pt0) cc_final: 0.7865 (pt0) REVERT: B 256 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 421 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9143 (mp) REVERT: B 533 ILE cc_start: 0.8661 (mt) cc_final: 0.8335 (mt) REVERT: B 537 PHE cc_start: 0.8430 (m-80) cc_final: 0.8221 (m-80) REVERT: B 592 ARG cc_start: 0.7877 (tpt-90) cc_final: 0.7468 (tpt-90) REVERT: B 626 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7445 (mmm160) REVERT: B 628 TRP cc_start: 0.8098 (m100) cc_final: 0.7716 (t-100) REVERT: B 742 MET cc_start: 0.9112 (mmt) cc_final: 0.8740 (mmt) REVERT: B 772 GLN cc_start: 0.7990 (tp40) cc_final: 0.6962 (tm-30) REVERT: C 12 GLN cc_start: 0.8083 (pt0) cc_final: 0.7866 (pt0) REVERT: C 256 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 537 PHE cc_start: 0.8684 (m-10) cc_final: 0.8337 (m-80) REVERT: C 630 MET cc_start: 0.8829 (mmm) cc_final: 0.8487 (mtm) REVERT: C 742 MET cc_start: 0.9117 (mmt) cc_final: 0.8750 (mmt) REVERT: C 772 GLN cc_start: 0.7991 (tp40) cc_final: 0.7001 (tm-30) REVERT: D 12 GLN cc_start: 0.8080 (pt0) cc_final: 0.7864 (pt0) REVERT: D 256 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 641 ILE cc_start: 0.9118 (mm) cc_final: 0.8737 (pt) REVERT: D 742 MET cc_start: 0.9095 (mmt) cc_final: 0.8721 (mmt) REVERT: D 772 GLN cc_start: 0.7991 (tp40) cc_final: 0.6999 (tm-30) outliers start: 37 outliers final: 33 residues processed: 391 average time/residue: 0.1391 time to fit residues: 88.9190 Evaluate side-chains 388 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 739 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 179 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN D 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103881 restraints weight = 43169.560| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.70 r_work: 0.3249 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23648 Z= 0.111 Angle : 0.586 12.497 31948 Z= 0.286 Chirality : 0.038 0.144 3540 Planarity : 0.004 0.045 4008 Dihedral : 7.768 83.304 3420 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.64 % Allowed : 19.20 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.16), residues: 2736 helix: 2.51 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -0.16 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 592 TYR 0.064 0.002 TYR C 636 PHE 0.025 0.001 PHE B 537 TRP 0.035 0.002 TRP B 485 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (23636) covalent geometry : angle 0.58599 / 0.29 (31948) hydrogen bonds : bond 0.03269 / 2.18 ( 1500) hydrogen bonds : angle 3.47300 / 2.49 ( 4452) metal coordination : bond 0.00057 / 0.04 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8097 (pt0) cc_final: 0.7879 (pt0) REVERT: A 256 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 533 ILE cc_start: 0.8569 (mt) cc_final: 0.7965 (mt) REVERT: A 537 PHE cc_start: 0.8663 (m-10) cc_final: 0.8322 (m-80) REVERT: A 592 ARG cc_start: 0.7799 (tpt-90) cc_final: 0.7435 (tpt-90) REVERT: A 742 MET cc_start: 0.9099 (mmt) cc_final: 0.8726 (mmt) REVERT: A 772 GLN cc_start: 0.7979 (tp40) cc_final: 0.7002 (tm-30) REVERT: B 32 ASP cc_start: 0.8561 (t0) cc_final: 0.7784 (p0) REVERT: B 256 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 421 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9108 (mp) REVERT: B 592 ARG cc_start: 0.7878 (tpt-90) cc_final: 0.7383 (tpt-90) REVERT: B 626 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7437 (mmm160) REVERT: B 742 MET cc_start: 0.9101 (mmt) cc_final: 0.8727 (mmt) REVERT: B 772 GLN cc_start: 0.7998 (tp40) cc_final: 0.7000 (tm-30) REVERT: C 226 GLU cc_start: 0.8545 (pm20) cc_final: 0.8323 (pm20) REVERT: C 256 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 537 PHE cc_start: 0.8653 (m-10) cc_final: 0.8338 (m-80) REVERT: C 630 MET cc_start: 0.8849 (mmm) cc_final: 0.8608 (mtm) REVERT: C 742 MET cc_start: 0.9104 (mmt) cc_final: 0.8734 (mmt) REVERT: C 772 GLN cc_start: 0.7963 (tp40) cc_final: 0.6987 (tm-30) REVERT: D 256 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 630 MET cc_start: 0.8854 (mmm) cc_final: 0.8602 (mtt) REVERT: D 641 ILE cc_start: 0.9139 (mm) cc_final: 0.8800 (pt) REVERT: D 742 MET cc_start: 0.9098 (mmt) cc_final: 0.8726 (mmt) REVERT: D 772 GLN cc_start: 0.7971 (tp40) cc_final: 0.6996 (tm-30) outliers start: 41 outliers final: 36 residues processed: 395 average time/residue: 0.1414 time to fit residues: 91.6695 Evaluate side-chains 384 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 347 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 739 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 260 optimal weight: 0.3980 chunk 232 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN B 12 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN D 12 GLN ** D 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101503 restraints weight = 43664.774| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.74 r_work: 0.3216 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23648 Z= 0.168 Angle : 0.621 12.173 31948 Z= 0.308 Chirality : 0.040 0.145 3540 Planarity : 0.004 0.045 4008 Dihedral : 8.003 84.684 3420 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.88 % Allowed : 18.84 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.16), residues: 2736 helix: 2.42 (0.11), residues: 2036 sheet: None (None), residues: 0 loop : -0.15 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 592 TYR 0.063 0.002 TYR C 636 PHE 0.024 0.002 PHE B 633 TRP 0.034 0.002 TRP D 485 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (23636) covalent geometry : angle 0.62090 / 0.31 (31948) hydrogen bonds : bond 0.03679 / 2.45 ( 1500) hydrogen bonds : angle 3.63859 / 2.61 ( 4452) metal coordination : bond 0.00126 / 0.09 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.30 seconds wall clock time: 82 minutes 52.18 seconds (4972.18 seconds total)