Starting phenix.real_space_refine on Sat Aug 8 08:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.map" model { file = "/net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvz_48675/08_2026/9mvz_48675.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 180 5.16 5 C 16812 2.51 5 N 4401 2.21 5 O 5019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 26415 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.22 Number of scatterers: 26415 At special positions: 0 Unit cell: (126.26, 118.77, 257.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 3 15.00 O 5019 8.00 N 4401 7.00 C 16812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 593 " - pdb=" SG CYS D 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS E 593 " - pdb=" SG CYS E 599 " distance=2.03 Simple disulfide: pdb=" SG CYS F 593 " - pdb=" SG CYS F 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 133 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6486 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 12 sheets defined 69.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 33 through 52 removed outlier: 4.033A pdb=" N VAL D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.777A pdb=" N ALA D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 142' Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 205 through 226 Processing helix chain 'D' and resid 227 through 255 removed outlier: 3.629A pdb=" N TYR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 294 Processing helix chain 'D' and resid 296 through 325 removed outlier: 5.338A pdb=" N HIS D 310 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 337 through 366 Proline residue: D 357 - end of helix removed outlier: 3.764A pdb=" N ARG D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 391 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.603A pdb=" N ILE D 395 " --> pdb=" O TRP D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.824A pdb=" N LEU D 423 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 440 removed outlier: 3.890A pdb=" N HIS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 460 through 476 removed outlier: 3.730A pdb=" N VAL D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 Processing helix chain 'D' and resid 507 through 513 Processing helix chain 'D' and resid 513 through 576 Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 598 through 673 Proline residue: D 624 - end of helix removed outlier: 3.602A pdb=" N MET D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Proline residue: D 634 - end of helix Proline residue: D 641 - end of helix removed outlier: 3.640A pdb=" N ILE D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 685 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 711 removed outlier: 3.611A pdb=" N LYS D 708 " --> pdb=" O GLN D 704 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 711 " --> pdb=" O MET D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 749 removed outlier: 4.307A pdb=" N MET D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 738 " --> pdb=" O THR D 734 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 798 Processing helix chain 'D' and resid 799 through 827 removed outlier: 3.974A pdb=" N ALA D 803 " --> pdb=" O ALA D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 864 removed outlier: 4.195A pdb=" N MET D 840 " --> pdb=" O MET D 836 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 844 " --> pdb=" O MET D 840 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 847 " --> pdb=" O ILE D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 896 removed outlier: 5.177A pdb=" N ALA D 881 " --> pdb=" O VAL D 877 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL D 882 " --> pdb=" O GLY D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 900 Processing helix chain 'D' and resid 902 through 923 removed outlier: 3.658A pdb=" N GLY D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 936 Processing helix chain 'D' and resid 937 through 941 removed outlier: 3.524A pdb=" N TRP D 940 " --> pdb=" O ARG D 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 20 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 40 through 56 Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.511A pdb=" N GLY G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 82 Processing helix chain 'C' and resid 5 through 27 removed outlier: 3.959A pdb=" N THR C 27 " --> pdb=" O MET C 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 33 through 52 removed outlier: 4.056A pdb=" N VAL E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'E' and resid 104 through 121 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.719A pdb=" N ALA E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 205 through 226 Processing helix chain 'E' and resid 227 through 255 removed outlier: 3.647A pdb=" N TYR E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 294 Processing helix chain 'E' and resid 296 through 325 removed outlier: 5.347A pdb=" N HIS E 310 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'E' and resid 337 through 366 removed outlier: 3.544A pdb=" N GLY E 356 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Proline residue: E 357 - end of helix removed outlier: 3.735A pdb=" N ARG E 365 " --> pdb=" O SER E 361 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.595A pdb=" N ILE E 395 " --> pdb=" O TRP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 413 Proline residue: E 411 - end of helix Processing helix chain 'E' and resid 418 through 423 removed outlier: 3.808A pdb=" N LEU E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 440 removed outlier: 3.877A pdb=" N HIS E 439 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 Processing helix chain 'E' and resid 460 through 476 removed outlier: 3.709A pdb=" N VAL E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 505 Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 513 through 576 Processing helix chain 'E' and resid 580 through 590 Processing helix chain 'E' and resid 598 through 673 Proline residue: E 624 - end of helix Proline residue: E 634 - end of helix removed outlier: 3.681A pdb=" N MET E 640 " --> pdb=" O MET E 636 " (cutoff:3.500A) Proline residue: E 641 - end of helix removed outlier: 3.680A pdb=" N ILE E 644 " --> pdb=" O MET E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 685 Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'E' and resid 700 through 711 removed outlier: 3.578A pdb=" N LYS E 708 " --> pdb=" O GLN E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 735 Processing helix chain 'E' and resid 736 through 749 Processing helix chain 'E' and resid 763 through 798 Processing helix chain 'E' and resid 799 through 827 removed outlier: 3.974A pdb=" N ALA E 803 " --> pdb=" O ALA E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 864 removed outlier: 4.133A pdb=" N MET E 840 " --> pdb=" O MET E 836 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 844 " --> pdb=" O MET E 840 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA E 847 " --> pdb=" O ILE E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 896 removed outlier: 5.216A pdb=" N ALA E 881 " --> pdb=" O VAL E 877 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL E 882 " --> pdb=" O GLY E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 900 Processing helix chain 'E' and resid 902 through 923 removed outlier: 3.536A pdb=" N GLY E 906 " --> pdb=" O LEU E 902 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 936 Processing helix chain 'E' and resid 937 through 941 removed outlier: 3.506A pdb=" N TRP E 940 " --> pdb=" O ARG E 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.079A pdb=" N VAL F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 71 through 84 Processing helix chain 'F' and resid 104 through 121 Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.773A pdb=" N ALA F 141 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 177 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 205 through 226 Processing helix chain 'F' and resid 227 through 255 removed outlier: 3.625A pdb=" N TYR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 294 Processing helix chain 'F' and resid 296 through 325 removed outlier: 5.351A pdb=" N HIS F 310 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 337 through 366 Proline residue: F 357 - end of helix removed outlier: 3.722A pdb=" N ARG F 365 " --> pdb=" O SER F 361 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 391 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.594A pdb=" N ILE F 395 " --> pdb=" O TRP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.829A pdb=" N LEU F 423 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 438 Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 460 through 476 removed outlier: 3.706A pdb=" N VAL F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 505 Processing helix chain 'F' and resid 507 through 513 Processing helix chain 'F' and resid 513 through 576 Processing helix chain 'F' and resid 580 through 590 Processing helix chain 'F' and resid 598 through 640 Proline residue: F 624 - end of helix Proline residue: F 634 - end of helix removed outlier: 3.747A pdb=" N MET F 640 " --> pdb=" O MET F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 673 removed outlier: 3.725A pdb=" N ILE F 644 " --> pdb=" O MET F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 685 Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 700 through 711 removed outlier: 3.602A pdb=" N LYS F 708 " --> pdb=" O GLN F 704 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET F 711 " --> pdb=" O MET F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 735 Processing helix chain 'F' and resid 736 through 749 Processing helix chain 'F' and resid 763 through 798 Processing helix chain 'F' and resid 799 through 827 removed outlier: 3.931A pdb=" N ALA F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 864 removed outlier: 4.140A pdb=" N MET F 840 " --> pdb=" O MET F 836 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 844 " --> pdb=" O MET F 840 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA F 847 " --> pdb=" O ILE F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 867 through 896 removed outlier: 5.194A pdb=" N ALA F 881 " --> pdb=" O VAL F 877 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL F 882 " --> pdb=" O GLY F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 900 Processing helix chain 'F' and resid 902 through 923 removed outlier: 3.657A pdb=" N GLY F 906 " --> pdb=" O LEU F 902 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 936 Processing helix chain 'F' and resid 937 through 941 Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 23 through 27 Processing helix chain 'H' and resid 40 through 56 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.517A pdb=" N GLY H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 23 through 27 Processing helix chain 'I' and resid 40 through 56 Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.537A pdb=" N GLY I 66 " --> pdb=" O GLU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 82 Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.506A pdb=" N VAL A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.662A pdb=" N THR B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.501A pdb=" N HIS D 127 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 152 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER D 91 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 480 through 484 removed outlier: 7.017A pdb=" N ILE D 723 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL D 483 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR D 721 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 35 " --> pdb=" O ILE D 758 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O ILE F 758 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR F 721 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL F 483 " --> pdb=" O THR F 721 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 723 " --> pdb=" O ALA F 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.795A pdb=" N ILE C 108 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 123 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS C 110 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 121 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 112 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 81 removed outlier: 3.533A pdb=" N ILE C 65 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER C 79 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 63 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS C 98 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.504A pdb=" N HIS E 127 " --> pdb=" O TYR E 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN E 152 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER E 91 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 480 through 484 removed outlier: 7.059A pdb=" N ILE E 723 " --> pdb=" O ALA E 481 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL E 483 " --> pdb=" O THR E 721 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 721 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 35 " --> pdb=" O ILE E 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 125 through 129 removed outlier: 4.295A pdb=" N GLN F 152 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER F 91 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 90 removed outlier: 6.803A pdb=" N ILE A 108 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR A 123 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS A 110 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 121 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 112 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 74 through 81 removed outlier: 3.527A pdb=" N ILE A 65 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 79 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 63 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS A 98 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.820A pdb=" N ILE B 108 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 123 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 110 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 121 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 112 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 81 removed outlier: 4.320A pdb=" N SER B 79 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS B 98 " --> pdb=" O MET B 68 " (cutoff:3.500A) 1953 hydrogen bonds defined for protein. 5682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.82 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8700 1.34 - 1.46: 5814 1.46 - 1.58: 12064 1.58 - 1.71: 2 1.71 - 1.83: 342 Bond restraints: 26922 Sorted by residual: bond pdb=" O27 PNS I 101 " pdb=" P24 PNS I 101 " ideal model delta sigma weight residual 1.704 1.829 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O27 PNS G 101 " pdb=" P24 PNS G 101 " ideal model delta sigma weight residual 1.704 1.829 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O27 PNS H 101 " pdb=" P24 PNS H 101 " ideal model delta sigma weight residual 1.704 1.828 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C34 PNS H 101 " pdb=" N36 PNS H 101 " ideal model delta sigma weight residual 1.337 1.410 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C34 PNS G 101 " pdb=" N36 PNS G 101 " ideal model delta sigma weight residual 1.337 1.409 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 26917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 36039 1.59 - 3.18: 524 3.18 - 4.76: 100 4.76 - 6.35: 37 6.35 - 7.94: 5 Bond angle restraints: 36705 Sorted by residual: angle pdb=" C THR E 498 " pdb=" N ILE E 499 " pdb=" CA ILE E 499 " ideal model delta sigma weight residual 120.24 122.87 -2.63 6.30e-01 2.52e+00 1.75e+01 angle pdb=" C THR F 498 " pdb=" N ILE F 499 " pdb=" CA ILE F 499 " ideal model delta sigma weight residual 120.24 122.85 -2.61 6.30e-01 2.52e+00 1.71e+01 angle pdb=" N ILE A 5 " pdb=" CA ILE A 5 " pdb=" C ILE A 5 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" C THR D 498 " pdb=" N ILE D 499 " pdb=" CA ILE D 499 " ideal model delta sigma weight residual 120.33 122.79 -2.46 8.00e-01 1.56e+00 9.49e+00 angle pdb=" C ILE E 499 " pdb=" CA ILE E 499 " pdb=" CB ILE E 499 " ideal model delta sigma weight residual 114.35 111.33 3.02 1.06e+00 8.90e-01 8.11e+00 ... (remaining 36700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 15313 16.62 - 33.24: 660 33.24 - 49.85: 138 49.85 - 66.47: 46 66.47 - 83.09: 4 Dihedral angle restraints: 16161 sinusoidal: 6120 harmonic: 10041 Sorted by residual: dihedral pdb=" CA ILE E 596 " pdb=" C ILE E 596 " pdb=" N PRO E 597 " pdb=" CA PRO E 597 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP D 565 " pdb=" CB ASP D 565 " pdb=" CG ASP D 565 " pdb=" OD1 ASP D 565 " ideal model delta sinusoidal sigma weight residual -30.00 -86.03 56.03 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ILE F 596 " pdb=" C ILE F 596 " pdb=" N PRO F 597 " pdb=" CA PRO F 597 " ideal model delta harmonic sigma weight residual -180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 16158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2885 0.034 - 0.067: 1061 0.067 - 0.101: 279 0.101 - 0.135: 140 0.135 - 0.168: 6 Chirality restraints: 4371 Sorted by residual: chirality pdb=" C32 PNS G 101 " pdb=" C29 PNS G 101 " pdb=" C34 PNS G 101 " pdb=" O33 PNS G 101 " both_signs ideal model delta sigma weight residual False 2.33 2.50 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" C32 PNS I 101 " pdb=" C29 PNS I 101 " pdb=" C34 PNS I 101 " pdb=" O33 PNS I 101 " both_signs ideal model delta sigma weight residual False 2.33 2.49 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" C32 PNS H 101 " pdb=" C29 PNS H 101 " pdb=" C34 PNS H 101 " pdb=" O33 PNS H 101 " both_signs ideal model delta sigma weight residual False 2.33 2.49 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 4368 not shown) Planarity restraints: 4707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 356 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 357 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 357 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 357 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 52 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO D 53 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 53 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 53 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 71 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO F 72 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 72 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 72 " 0.019 5.00e-02 4.00e+02 ... (remaining 4704 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5543 2.78 - 3.31: 26177 3.31 - 3.84: 44310 3.84 - 4.37: 50544 4.37 - 4.90: 90316 Nonbonded interactions: 216890 Sorted by model distance: nonbonded pdb=" OH TYR D 111 " pdb=" OD1 ASP D 130 " model vdw 2.244 3.040 nonbonded pdb=" O ILE E 748 " pdb=" OG1 THR E 751 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" OD1 ASP E 130 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" OD1 ASP F 130 " model vdw 2.260 3.040 nonbonded pdb=" O ILE D 748 " pdb=" OG1 THR D 751 " model vdw 2.273 3.040 ... (remaining 216885 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 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: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 26928 Z= 0.219 Angle : 0.545 7.941 36717 Z= 0.297 Chirality : 0.041 0.168 4371 Planarity : 0.004 0.037 4707 Dihedral : 10.487 83.091 9657 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.42 % Allowed : 3.13 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.03 (0.14), residues: 3450 helix: 2.68 (0.11), residues: 2196 sheet: 1.90 (0.30), residues: 324 loop : 0.41 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 23 TYR 0.012 0.001 TYR D 767 PHE 0.010 0.001 PHE E 720 TRP 0.013 0.001 TRP E 381 HIS 0.002 0.001 HIS F 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (26922) covalent geometry : angle 0.54461 / 0.30 (36705) SS BOND : bond 0.00379 / 0.24 ( 6) SS BOND : angle 1.32766 / 0.96 ( 12) hydrogen bonds : bond 0.14508 / 9.67 ( 1953) hydrogen bonds : angle 5.25616 / 3.77 ( 5682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 611 time to evaluate : 0.980 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: D 64 VAL cc_start: 0.9164 (t) cc_final: 0.8919 (m) REVERT: D 335 GLN cc_start: 0.8230 (tt0) cc_final: 0.7840 (tm-30) REVERT: D 544 ILE cc_start: 0.8920 (mt) cc_final: 0.8718 (mp) REVERT: D 577 ASP cc_start: 0.1808 (OUTLIER) cc_final: 0.1400 (m-30) REVERT: D 925 SER cc_start: 0.9243 (m) cc_final: 0.8949 (p) REVERT: G 31 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8441 (mmmm) REVERT: C 62 SER cc_start: 0.8499 (p) cc_final: 0.7920 (t) REVERT: C 100 MET cc_start: 0.8621 (mtp) cc_final: 0.8412 (mtp) REVERT: C 119 LYS cc_start: 0.9272 (mmtt) cc_final: 0.9021 (mmtm) REVERT: C 127 MET cc_start: 0.7093 (ttm) cc_final: 0.5940 (ttm) REVERT: E 577 ASP cc_start: 0.4108 (OUTLIER) cc_final: 0.2505 (m-30) REVERT: E 777 ASP cc_start: 0.7707 (m-30) cc_final: 0.7484 (m-30) REVERT: E 794 MET cc_start: 0.8409 (ttp) cc_final: 0.8141 (ttp) REVERT: E 814 LEU cc_start: 0.8859 (tp) cc_final: 0.8649 (tp) REVERT: E 925 SER cc_start: 0.9237 (m) cc_final: 0.9031 (p) REVERT: F 112 ASP cc_start: 0.7772 (m-30) cc_final: 0.7524 (m-30) REVERT: F 541 MET cc_start: 0.8433 (tpt) cc_final: 0.8011 (tpt) REVERT: F 699 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7304 (mm-30) REVERT: F 777 ASP cc_start: 0.7811 (m-30) cc_final: 0.7437 (m-30) REVERT: H 31 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8473 (mmmm) REVERT: H 36 ASP cc_start: 0.8573 (m-30) cc_final: 0.8372 (m-30) REVERT: H 62 GLU cc_start: 0.8603 (mp0) cc_final: 0.8338 (mp0) REVERT: H 69 THR cc_start: 0.8961 (p) cc_final: 0.8344 (p) REVERT: I 25 SER cc_start: 0.9435 (p) cc_final: 0.7852 (p) REVERT: I 26 GLU cc_start: 0.8429 (tp30) cc_final: 0.8178 (tp30) REVERT: I 31 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8381 (mmmm) REVERT: I 62 GLU cc_start: 0.8611 (mp0) cc_final: 0.8358 (mp0) REVERT: A 28 VAL cc_start: 0.7801 (t) cc_final: 0.7488 (t) REVERT: A 62 SER cc_start: 0.8481 (p) cc_final: 0.7989 (t) REVERT: B 62 SER cc_start: 0.8675 (p) cc_final: 0.8106 (t) outliers start: 68 outliers final: 11 residues processed: 667 average time/residue: 0.6579 time to fit residues: 508.1688 Evaluate side-chains 483 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 470 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 779 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN D 496 HIS D 645 GLN D 652 GLN D 674 ASN C 128 ASN E 82 GLN E 496 HIS E 652 GLN E 674 ASN F 82 GLN F 496 HIS A 128 ASN B 128 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.073318 restraints weight = 43039.531| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.42 r_work: 0.2785 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26928 Z= 0.146 Angle : 0.542 8.811 36717 Z= 0.284 Chirality : 0.041 0.154 4371 Planarity : 0.004 0.052 4707 Dihedral : 4.931 58.521 3756 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.31 % Allowed : 10.92 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.17 (0.14), residues: 3450 helix: 2.82 (0.11), residues: 2187 sheet: 1.71 (0.30), residues: 306 loop : 0.55 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 68 TYR 0.019 0.001 TYR I 76 PHE 0.014 0.001 PHE F 580 TRP 0.011 0.001 TRP D 600 HIS 0.015 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (26922) covalent geometry : angle 0.54019 / 0.28 (36705) SS BOND : bond 0.00185 / 0.15 ( 6) SS BOND : angle 2.48321 / 1.84 ( 12) hydrogen bonds : bond 0.05633 / 3.90 ( 1953) hydrogen bonds : angle 4.31289 / 3.11 ( 5682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 514 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7460 (mpp-170) REVERT: D 64 VAL cc_start: 0.9319 (t) cc_final: 0.8963 (m) REVERT: D 237 MET cc_start: 0.9012 (mtm) cc_final: 0.8716 (mtm) REVERT: D 335 GLN cc_start: 0.8689 (tt0) cc_final: 0.8160 (tm-30) REVERT: D 541 MET cc_start: 0.8464 (tpp) cc_final: 0.8042 (tpt) REVERT: D 544 ILE cc_start: 0.8545 (mt) cc_final: 0.8339 (mp) REVERT: D 602 MET cc_start: 0.2671 (ptp) cc_final: 0.2397 (mtm) REVERT: D 709 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8435 (mp) REVERT: D 777 ASP cc_start: 0.8527 (m-30) cc_final: 0.8240 (m-30) REVERT: G 7 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8594 (mt-10) REVERT: G 18 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: G 26 GLU cc_start: 0.8757 (tp30) cc_final: 0.8232 (tp30) REVERT: G 31 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8337 (mmmm) REVERT: G 36 ASP cc_start: 0.8807 (m-30) cc_final: 0.8605 (m-30) REVERT: C 23 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mpp) REVERT: C 62 SER cc_start: 0.8659 (p) cc_final: 0.7991 (t) REVERT: C 121 GLU cc_start: 0.9268 (tt0) cc_final: 0.8866 (tt0) REVERT: C 122 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8291 (mtp-110) REVERT: E 25 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8088 (pmt-80) REVERT: E 295 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: E 335 GLN cc_start: 0.8727 (tt0) cc_final: 0.8463 (tm-30) REVERT: E 559 MET cc_start: 0.6825 (tmm) cc_final: 0.6121 (tmt) REVERT: E 577 ASP cc_start: 0.2613 (OUTLIER) cc_final: 0.2173 (m-30) REVERT: E 777 ASP cc_start: 0.8541 (m-30) cc_final: 0.8334 (m-30) REVERT: E 824 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8908 (tp) REVERT: F 25 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7654 (mpp-170) REVERT: F 112 ASP cc_start: 0.8752 (m-30) cc_final: 0.8427 (m-30) REVERT: F 541 MET cc_start: 0.8578 (tpt) cc_final: 0.8322 (tpt) REVERT: F 544 ILE cc_start: 0.8232 (mt) cc_final: 0.7940 (mp) REVERT: F 555 MET cc_start: 0.8577 (mtt) cc_final: 0.8260 (ppp) REVERT: F 688 ASP cc_start: 0.9132 (p0) cc_final: 0.8838 (p0) REVERT: F 699 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8343 (mm-30) REVERT: F 777 ASP cc_start: 0.8461 (m-30) cc_final: 0.8168 (m-30) REVERT: H 17 GLU cc_start: 0.8787 (tp30) cc_final: 0.8412 (tp30) REVERT: H 18 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: H 25 SER cc_start: 0.9114 (p) cc_final: 0.8831 (p) REVERT: H 26 GLU cc_start: 0.8785 (tp30) cc_final: 0.8455 (tp30) REVERT: H 31 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8538 (mmmm) REVERT: H 36 ASP cc_start: 0.8526 (m-30) cc_final: 0.8285 (m-30) REVERT: I 7 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8429 (mp0) REVERT: I 25 SER cc_start: 0.9079 (p) cc_final: 0.8789 (p) REVERT: I 26 GLU cc_start: 0.9009 (tp30) cc_final: 0.8508 (tp30) REVERT: I 31 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8398 (mmmm) REVERT: A 23 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7506 (mpt) REVERT: A 62 SER cc_start: 0.8793 (p) cc_final: 0.8079 (t) REVERT: B 62 SER cc_start: 0.8769 (p) cc_final: 0.8092 (t) REVERT: B 71 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8308 (pt0) REVERT: B 127 MET cc_start: 0.8451 (ttm) cc_final: 0.8156 (ttp) outliers start: 93 outliers final: 28 residues processed: 555 average time/residue: 0.6117 time to fit residues: 395.5222 Evaluate side-chains 508 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 469 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 779 ILE Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 169 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 652 GLN D 680 GLN F 652 GLN A 66 ASN B 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.072297 restraints weight = 43243.443| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.43 r_work: 0.2766 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26928 Z= 0.172 Angle : 0.547 11.249 36717 Z= 0.282 Chirality : 0.041 0.141 4371 Planarity : 0.004 0.044 4707 Dihedral : 4.715 57.875 3754 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.17 % Allowed : 13.16 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.12 (0.14), residues: 3450 helix: 2.79 (0.11), residues: 2187 sheet: 1.60 (0.31), residues: 306 loop : 0.53 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 456 TYR 0.014 0.001 TYR E 516 PHE 0.013 0.001 PHE D 110 TRP 0.010 0.001 TRP E 381 HIS 0.011 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (26922) covalent geometry : angle 0.54526 / 0.28 (36705) SS BOND : bond 0.00546 / 0.33 ( 6) SS BOND : angle 2.52693 / 1.97 ( 12) hydrogen bonds : bond 0.05593 / 3.88 ( 1953) hydrogen bonds : angle 4.20580 / 3.04 ( 5682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 473 time to evaluate : 0.992 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: D 129 GLN cc_start: 0.8628 (pt0) cc_final: 0.8345 (tt0) REVERT: D 237 MET cc_start: 0.9032 (mtm) cc_final: 0.8480 (mtt) REVERT: D 335 GLN cc_start: 0.8712 (tt0) cc_final: 0.8199 (tm-30) REVERT: D 598 MET cc_start: 0.3517 (OUTLIER) cc_final: 0.2004 (mtm) REVERT: D 602 MET cc_start: 0.2637 (ptp) cc_final: 0.2422 (mtm) REVERT: D 629 MET cc_start: 0.7595 (tmm) cc_final: 0.7384 (tmm) REVERT: D 709 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8468 (mp) REVERT: D 777 ASP cc_start: 0.8542 (m-30) cc_final: 0.8236 (m-30) REVERT: D 824 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8907 (tp) REVERT: G 26 GLU cc_start: 0.8655 (tp30) cc_final: 0.8152 (tp30) REVERT: G 31 LYS cc_start: 0.8941 (mmtp) cc_final: 0.8421 (mmmm) REVERT: G 36 ASP cc_start: 0.8811 (m-30) cc_final: 0.8539 (m-30) REVERT: C 62 SER cc_start: 0.8695 (p) cc_final: 0.8029 (t) REVERT: C 121 GLU cc_start: 0.9242 (tt0) cc_final: 0.8909 (tt0) REVERT: E 295 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: E 577 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2239 (m-30) REVERT: E 777 ASP cc_start: 0.8560 (m-30) cc_final: 0.8346 (m-30) REVERT: E 824 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8876 (tp) REVERT: F 112 ASP cc_start: 0.8787 (m-30) cc_final: 0.8457 (m-30) REVERT: F 555 MET cc_start: 0.8495 (mtt) cc_final: 0.8274 (pp-130) REVERT: F 559 MET cc_start: 0.5488 (tmt) cc_final: 0.5106 (tmt) REVERT: F 602 MET cc_start: 0.2824 (ptp) cc_final: 0.1570 (mpp) REVERT: F 688 ASP cc_start: 0.9121 (p0) cc_final: 0.8854 (p0) REVERT: F 699 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8401 (mm-30) REVERT: H 17 GLU cc_start: 0.8806 (tp30) cc_final: 0.8465 (tp30) REVERT: H 25 SER cc_start: 0.9107 (p) cc_final: 0.8803 (p) REVERT: H 26 GLU cc_start: 0.8801 (tp30) cc_final: 0.8329 (tp30) REVERT: H 31 LYS cc_start: 0.9007 (mmtp) cc_final: 0.8468 (mmmm) REVERT: H 36 ASP cc_start: 0.8603 (m-30) cc_final: 0.8318 (m-30) REVERT: I 25 SER cc_start: 0.9094 (p) cc_final: 0.8809 (p) REVERT: I 26 GLU cc_start: 0.9032 (tp30) cc_final: 0.8436 (tp30) REVERT: I 31 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8314 (mmmm) REVERT: A 23 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7464 (mpt) REVERT: A 55 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 62 SER cc_start: 0.8827 (p) cc_final: 0.8127 (t) REVERT: B 62 SER cc_start: 0.8775 (p) cc_final: 0.8106 (t) REVERT: B 120 GLU cc_start: 0.9096 (tp30) cc_final: 0.8850 (tp30) REVERT: B 127 MET cc_start: 0.8455 (ttm) cc_final: 0.8201 (tmm) outliers start: 89 outliers final: 41 residues processed: 521 average time/residue: 0.5895 time to fit residues: 359.9699 Evaluate side-chains 493 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 445 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 340 optimal weight: 5.9990 chunk 264 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.0184 > 50:) chunk 109 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 323 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 620 GLN B 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071690 restraints weight = 43058.088| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.43 r_work: 0.2748 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26928 Z= 0.187 Angle : 0.559 9.630 36717 Z= 0.289 Chirality : 0.042 0.211 4371 Planarity : 0.004 0.058 4707 Dihedral : 4.745 57.232 3752 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.84 % Allowed : 13.98 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.03 (0.14), residues: 3450 helix: 2.71 (0.11), residues: 2190 sheet: 1.45 (0.31), residues: 306 loop : 0.53 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 68 TYR 0.018 0.001 TYR I 76 PHE 0.012 0.001 PHE D 110 TRP 0.010 0.001 TRP E 381 HIS 0.008 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (26922) covalent geometry : angle 0.55438 / 0.29 (36705) SS BOND : bond 0.00669 / 0.39 ( 6) SS BOND : angle 3.98365 / 2.72 ( 12) hydrogen bonds : bond 0.05613 / 3.90 ( 1953) hydrogen bonds : angle 4.20263 / 3.04 ( 5682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 446 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9109 (m) REVERT: D 237 MET cc_start: 0.9057 (mtm) cc_final: 0.8490 (mtt) REVERT: D 335 GLN cc_start: 0.8720 (tt0) cc_final: 0.8203 (tm-30) REVERT: D 390 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.7290 (tmt-80) REVERT: D 598 MET cc_start: 0.3694 (OUTLIER) cc_final: 0.1740 (mtm) REVERT: D 626 MET cc_start: 0.7062 (mmt) cc_final: 0.6551 (tpp) REVERT: D 629 MET cc_start: 0.7768 (tmm) cc_final: 0.7431 (tmm) REVERT: D 636 MET cc_start: 0.7775 (mmt) cc_final: 0.7349 (mmp) REVERT: D 709 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8416 (mp) REVERT: D 777 ASP cc_start: 0.8511 (m-30) cc_final: 0.8179 (m-30) REVERT: D 824 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8918 (tp) REVERT: G 7 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8617 (mt-10) REVERT: G 23 GLU cc_start: 0.8358 (tp30) cc_final: 0.7851 (tp30) REVERT: G 26 GLU cc_start: 0.8714 (tp30) cc_final: 0.8238 (tp30) REVERT: G 31 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8408 (mmmm) REVERT: G 36 ASP cc_start: 0.8828 (m-30) cc_final: 0.8561 (m-30) REVERT: C 23 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7465 (mpt) REVERT: C 62 SER cc_start: 0.8701 (p) cc_final: 0.8022 (t) REVERT: C 121 GLU cc_start: 0.9173 (tt0) cc_final: 0.8784 (tt0) REVERT: C 127 MET cc_start: 0.8517 (ttm) cc_final: 0.8288 (tmm) REVERT: E 295 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: E 577 ASP cc_start: 0.2557 (OUTLIER) cc_final: 0.2023 (m-30) REVERT: E 798 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8193 (mmt-90) REVERT: E 824 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8942 (tp) REVERT: F 377 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7123 (ptm-80) REVERT: F 559 MET cc_start: 0.5483 (tmt) cc_final: 0.5219 (tmt) REVERT: F 602 MET cc_start: 0.3026 (ptp) cc_final: 0.1705 (mpp) REVERT: F 688 ASP cc_start: 0.9110 (p0) cc_final: 0.8856 (p0) REVERT: F 699 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8317 (mm-30) REVERT: H 18 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: H 25 SER cc_start: 0.9106 (p) cc_final: 0.8900 (p) REVERT: H 31 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8753 (mmtp) REVERT: H 36 ASP cc_start: 0.8643 (m-30) cc_final: 0.8361 (m-30) REVERT: I 25 SER cc_start: 0.9097 (p) cc_final: 0.8796 (p) REVERT: I 26 GLU cc_start: 0.9015 (tp30) cc_final: 0.8431 (tp30) REVERT: I 31 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8317 (mmmm) REVERT: A 55 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8683 (mt-10) REVERT: A 62 SER cc_start: 0.8834 (p) cc_final: 0.8145 (t) REVERT: A 110 CYS cc_start: 0.6766 (p) cc_final: 0.6451 (p) REVERT: B 62 SER cc_start: 0.8746 (p) cc_final: 0.8071 (t) REVERT: B 127 MET cc_start: 0.8448 (ttm) cc_final: 0.8205 (tmm) outliers start: 108 outliers final: 49 residues processed: 509 average time/residue: 0.6073 time to fit residues: 361.1866 Evaluate side-chains 507 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 446 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 236 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 307 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 680 GLN B 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.073782 restraints weight = 42893.965| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.43 r_work: 0.2804 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26928 Z= 0.130 Angle : 0.530 10.178 36717 Z= 0.272 Chirality : 0.040 0.262 4371 Planarity : 0.004 0.043 4707 Dihedral : 4.629 57.230 3752 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.17 % Allowed : 15.12 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.18 (0.14), residues: 3450 helix: 2.82 (0.11), residues: 2205 sheet: 1.46 (0.31), residues: 306 loop : 0.61 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 944 TYR 0.015 0.001 TYR G 76 PHE 0.012 0.001 PHE F 110 TRP 0.009 0.001 TRP C 84 HIS 0.006 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (26922) covalent geometry : angle 0.52749 / 0.27 (36705) SS BOND : bond 0.00661 / 0.35 ( 6) SS BOND : angle 3.10420 / 2.26 ( 12) hydrogen bonds : bond 0.04990 / 3.47 ( 1953) hydrogen bonds : angle 4.07981 / 2.95 ( 5682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 465 time to evaluate : 1.112 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: D 237 MET cc_start: 0.8996 (mtm) cc_final: 0.8541 (mtt) REVERT: D 335 GLN cc_start: 0.8705 (tt0) cc_final: 0.8198 (tm-30) REVERT: D 374 ARG cc_start: 0.7800 (ptt180) cc_final: 0.6928 (ptp-170) REVERT: D 390 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.7262 (tmt-80) REVERT: D 555 MET cc_start: 0.8596 (ttm) cc_final: 0.8223 (ttm) REVERT: D 598 MET cc_start: 0.3983 (mmt) cc_final: 0.1857 (mtm) REVERT: D 629 MET cc_start: 0.7713 (tmm) cc_final: 0.7280 (tmm) REVERT: D 777 ASP cc_start: 0.8469 (m-30) cc_final: 0.8125 (m-30) REVERT: D 784 SER cc_start: 0.8696 (m) cc_final: 0.8390 (p) REVERT: D 824 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8855 (tp) REVERT: G 23 GLU cc_start: 0.8430 (tp30) cc_final: 0.8064 (tp30) REVERT: G 26 GLU cc_start: 0.8759 (tp30) cc_final: 0.8304 (tp30) REVERT: G 31 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8482 (mmmm) REVERT: G 36 ASP cc_start: 0.8836 (m-30) cc_final: 0.8533 (m-30) REVERT: C 62 SER cc_start: 0.8720 (p) cc_final: 0.8061 (t) REVERT: C 121 GLU cc_start: 0.9163 (tt0) cc_final: 0.8737 (tt0) REVERT: C 127 MET cc_start: 0.8564 (ttm) cc_final: 0.8360 (tmm) REVERT: E 70 ASP cc_start: 0.8904 (m-30) cc_final: 0.8583 (p0) REVERT: E 577 ASP cc_start: 0.2566 (OUTLIER) cc_final: 0.2061 (m-30) REVERT: E 798 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8145 (mmt-90) REVERT: E 824 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8900 (tp) REVERT: F 335 GLN cc_start: 0.8728 (tt0) cc_final: 0.8223 (tm-30) REVERT: F 374 ARG cc_start: 0.7830 (ptt180) cc_final: 0.7055 (ptp-170) REVERT: F 540 GLU cc_start: 0.8810 (tp30) cc_final: 0.8523 (tp30) REVERT: F 559 MET cc_start: 0.5453 (tmt) cc_final: 0.5153 (tmt) REVERT: F 602 MET cc_start: 0.2974 (ptp) cc_final: 0.1702 (mpp) REVERT: F 674 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9042 (t0) REVERT: F 688 ASP cc_start: 0.9016 (p0) cc_final: 0.8747 (p0) REVERT: F 699 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8255 (mm-30) REVERT: H 25 SER cc_start: 0.9102 (p) cc_final: 0.8879 (p) REVERT: H 31 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8767 (mmtp) REVERT: H 36 ASP cc_start: 0.8634 (m-30) cc_final: 0.8347 (m-30) REVERT: I 7 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: I 25 SER cc_start: 0.9066 (p) cc_final: 0.8757 (p) REVERT: I 26 GLU cc_start: 0.9001 (tp30) cc_final: 0.8454 (tp30) REVERT: I 31 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8235 (mmmm) REVERT: I 80 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mm) REVERT: A 55 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8692 (mt-10) REVERT: A 62 SER cc_start: 0.8886 (p) cc_final: 0.8249 (t) REVERT: B 62 SER cc_start: 0.8785 (p) cc_final: 0.8128 (t) REVERT: B 127 MET cc_start: 0.8418 (ttm) cc_final: 0.8185 (tmm) outliers start: 89 outliers final: 41 residues processed: 514 average time/residue: 0.5917 time to fit residues: 356.6664 Evaluate side-chains 505 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 456 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 620 GLN Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 538 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 639 VAL Chi-restraints excluded: chain F residue 674 ASN Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 69 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071454 restraints weight = 43465.955| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.45 r_work: 0.2736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26928 Z= 0.187 Angle : 0.572 10.061 36717 Z= 0.292 Chirality : 0.042 0.228 4371 Planarity : 0.004 0.042 4707 Dihedral : 4.602 57.313 3748 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.52 % Allowed : 16.04 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3.10 (0.14), residues: 3450 helix: 2.74 (0.11), residues: 2208 sheet: 1.48 (0.31), residues: 306 loop : 0.59 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 456 TYR 0.029 0.001 TYR I 76 PHE 0.011 0.001 PHE F 720 TRP 0.010 0.001 TRP E 381 HIS 0.005 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (26922) covalent geometry : angle 0.56885 / 0.29 (36705) SS BOND : bond 0.00267 / 0.17 ( 6) SS BOND : angle 3.53192 / 2.50 ( 12) hydrogen bonds : bond 0.05493 / 3.81 ( 1953) hydrogen bonds : angle 4.15797 / 3.01 ( 5682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 438 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 237 MET cc_start: 0.8956 (mtm) cc_final: 0.8517 (mtt) REVERT: D 335 GLN cc_start: 0.8648 (tt0) cc_final: 0.8135 (tm-30) REVERT: D 390 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.7304 (tmt-80) REVERT: D 555 MET cc_start: 0.8232 (ttm) cc_final: 0.7952 (tmt) REVERT: D 598 MET cc_start: 0.3723 (OUTLIER) cc_final: 0.2151 (mtm) REVERT: D 629 MET cc_start: 0.7750 (tmm) cc_final: 0.7247 (tmm) REVERT: D 784 SER cc_start: 0.8649 (m) cc_final: 0.8335 (p) REVERT: D 824 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8806 (tp) REVERT: G 7 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8310 (mp0) REVERT: G 23 GLU cc_start: 0.8527 (tp30) cc_final: 0.8114 (tp30) REVERT: G 26 GLU cc_start: 0.8732 (tp30) cc_final: 0.8231 (tp30) REVERT: G 31 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8466 (mmmm) REVERT: G 36 ASP cc_start: 0.8817 (m-30) cc_final: 0.8508 (m-30) REVERT: C 62 SER cc_start: 0.8549 (p) cc_final: 0.7874 (t) REVERT: C 121 GLU cc_start: 0.9086 (tt0) cc_final: 0.8691 (tt0) REVERT: C 127 MET cc_start: 0.8608 (ttm) cc_final: 0.8383 (tmm) REVERT: E 70 ASP cc_start: 0.8947 (m-30) cc_final: 0.8614 (p0) REVERT: E 178 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6215 (mtp85) REVERT: E 237 MET cc_start: 0.8876 (mtm) cc_final: 0.8593 (mtt) REVERT: E 445 MET cc_start: 0.9259 (mmp) cc_final: 0.8952 (mmm) REVERT: E 577 ASP cc_start: 0.2684 (OUTLIER) cc_final: 0.2156 (m-30) REVERT: E 794 MET cc_start: 0.8965 (ttp) cc_final: 0.8684 (mtm) REVERT: E 798 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8180 (mmt-90) REVERT: E 824 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8883 (tp) REVERT: F 374 ARG cc_start: 0.7844 (ptt180) cc_final: 0.6965 (ptp-170) REVERT: F 559 MET cc_start: 0.5441 (tmt) cc_final: 0.5155 (tmt) REVERT: F 602 MET cc_start: 0.2983 (ptp) cc_final: 0.2635 (tmm) REVERT: F 674 ASN cc_start: 0.9508 (t0) cc_final: 0.9076 (t0) REVERT: F 688 ASP cc_start: 0.9071 (p0) cc_final: 0.8821 (p0) REVERT: F 699 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8197 (mm-30) REVERT: H 25 SER cc_start: 0.9071 (p) cc_final: 0.8689 (p) REVERT: H 31 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8750 (mmtp) REVERT: H 36 ASP cc_start: 0.8622 (m-30) cc_final: 0.8348 (m-30) REVERT: I 7 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8291 (mp0) REVERT: I 25 SER cc_start: 0.9058 (p) cc_final: 0.8750 (p) REVERT: I 26 GLU cc_start: 0.9013 (tp30) cc_final: 0.8437 (tp30) REVERT: I 31 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8198 (mmmm) REVERT: A 55 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8683 (mt-10) REVERT: A 62 SER cc_start: 0.8749 (p) cc_final: 0.8101 (t) REVERT: B 62 SER cc_start: 0.8698 (p) cc_final: 0.8017 (t) REVERT: B 127 MET cc_start: 0.8363 (ttm) cc_final: 0.8117 (tmm) outliers start: 99 outliers final: 52 residues processed: 490 average time/residue: 0.5995 time to fit residues: 345.8057 Evaluate side-chains 497 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 438 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 538 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 639 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 274 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 340 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 339 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.073227 restraints weight = 43127.134| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.45 r_work: 0.2784 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26928 Z= 0.135 Angle : 0.553 13.084 36717 Z= 0.278 Chirality : 0.040 0.232 4371 Planarity : 0.004 0.045 4707 Dihedral : 4.539 56.493 3748 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.85 % Allowed : 17.18 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3.20 (0.14), residues: 3450 helix: 2.81 (0.11), residues: 2205 sheet: 1.50 (0.31), residues: 306 loop : 0.68 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 68 TYR 0.017 0.001 TYR F 586 PHE 0.011 0.001 PHE F 110 TRP 0.009 0.001 TRP C 84 HIS 0.006 0.001 HIS F 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26922) covalent geometry : angle 0.54964 / 0.28 (36705) SS BOND : bond 0.00586 / 0.29 ( 6) SS BOND : angle 3.17140 / 2.22 ( 12) hydrogen bonds : bond 0.04987 / 3.46 ( 1953) hydrogen bonds : angle 4.05506 / 2.94 ( 5682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 453 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 237 MET cc_start: 0.8936 (mtm) cc_final: 0.8537 (mtt) REVERT: D 335 GLN cc_start: 0.8630 (tt0) cc_final: 0.8126 (tm-30) REVERT: D 374 ARG cc_start: 0.7815 (ptt180) cc_final: 0.6834 (ptp-170) REVERT: D 390 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7259 (tmt-80) REVERT: D 540 GLU cc_start: 0.8923 (tp30) cc_final: 0.8680 (tp30) REVERT: D 555 MET cc_start: 0.8267 (ttm) cc_final: 0.7989 (tmt) REVERT: D 598 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.1862 (mtm) REVERT: D 629 MET cc_start: 0.7735 (tmm) cc_final: 0.7260 (tmm) REVERT: D 784 SER cc_start: 0.8641 (m) cc_final: 0.8333 (p) REVERT: D 824 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8802 (tp) REVERT: G 7 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8282 (mp0) REVERT: G 16 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8431 (mp) REVERT: G 23 GLU cc_start: 0.8516 (tp30) cc_final: 0.8125 (tp30) REVERT: G 26 GLU cc_start: 0.8730 (tp30) cc_final: 0.8165 (tp30) REVERT: G 31 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8503 (mmtm) REVERT: G 36 ASP cc_start: 0.8805 (m-30) cc_final: 0.8500 (m-30) REVERT: C 62 SER cc_start: 0.8577 (p) cc_final: 0.7909 (t) REVERT: C 127 MET cc_start: 0.8511 (ttm) cc_final: 0.8311 (tmm) REVERT: E 70 ASP cc_start: 0.8904 (m-30) cc_final: 0.8621 (p0) REVERT: E 178 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6231 (mtp85) REVERT: E 577 ASP cc_start: 0.3474 (OUTLIER) cc_final: 0.2544 (m-30) REVERT: E 615 MET cc_start: 0.2164 (mmt) cc_final: 0.1432 (mtt) REVERT: E 794 MET cc_start: 0.8948 (ttp) cc_final: 0.8636 (mtm) REVERT: E 798 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8165 (mmt-90) REVERT: E 824 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (tp) REVERT: F 335 GLN cc_start: 0.8686 (tt0) cc_final: 0.8178 (tm-30) REVERT: F 374 ARG cc_start: 0.7784 (ptt180) cc_final: 0.6985 (ptp-170) REVERT: F 540 GLU cc_start: 0.8802 (tp30) cc_final: 0.8490 (tp30) REVERT: F 559 MET cc_start: 0.5501 (tmt) cc_final: 0.5261 (tmt) REVERT: F 602 MET cc_start: 0.2964 (ptp) cc_final: 0.1718 (mpp) REVERT: F 628 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7991 (mtm-85) REVERT: F 674 ASN cc_start: 0.9508 (t0) cc_final: 0.9063 (t0) REVERT: F 688 ASP cc_start: 0.9020 (p0) cc_final: 0.8782 (p0) REVERT: F 699 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8147 (mm-30) REVERT: H 25 SER cc_start: 0.9073 (p) cc_final: 0.8779 (p) REVERT: H 31 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8767 (mmtp) REVERT: H 36 ASP cc_start: 0.8651 (m-30) cc_final: 0.8379 (m-30) REVERT: I 7 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: I 25 SER cc_start: 0.9038 (p) cc_final: 0.8725 (p) REVERT: I 26 GLU cc_start: 0.9008 (tp30) cc_final: 0.8438 (tp30) REVERT: I 31 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8223 (mmmm) REVERT: A 55 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 62 SER cc_start: 0.8771 (p) cc_final: 0.8135 (t) REVERT: B 62 SER cc_start: 0.8679 (p) cc_final: 0.8005 (t) REVERT: B 127 MET cc_start: 0.8318 (ttm) cc_final: 0.8098 (tmm) outliers start: 80 outliers final: 45 residues processed: 497 average time/residue: 0.5857 time to fit residues: 341.3023 Evaluate side-chains 499 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 445 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 639 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 324 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 620 GLN D 680 GLN F 645 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071417 restraints weight = 43450.994| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.44 r_work: 0.2741 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26928 Z= 0.199 Angle : 0.597 10.800 36717 Z= 0.302 Chirality : 0.042 0.191 4371 Planarity : 0.004 0.045 4707 Dihedral : 4.615 56.995 3748 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.09 % Allowed : 17.36 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3.07 (0.14), residues: 3450 helix: 2.69 (0.11), residues: 2208 sheet: 1.44 (0.30), residues: 330 loop : 0.67 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 68 TYR 0.020 0.001 TYR I 76 PHE 0.012 0.001 PHE F 703 TRP 0.010 0.001 TRP E 381 HIS 0.004 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (26922) covalent geometry : angle 0.59355 / 0.30 (36705) SS BOND : bond 0.00358 / 0.21 ( 6) SS BOND : angle 3.83246 / 2.64 ( 12) hydrogen bonds : bond 0.05570 / 3.86 ( 1953) hydrogen bonds : angle 4.14237 / 3.00 ( 5682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 445 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 237 MET cc_start: 0.8951 (mtm) cc_final: 0.8566 (mtt) REVERT: D 335 GLN cc_start: 0.8655 (tt0) cc_final: 0.8146 (tm-30) REVERT: D 390 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.7364 (tmt-80) REVERT: D 541 MET cc_start: 0.8395 (tpp) cc_final: 0.8075 (tpt) REVERT: D 555 MET cc_start: 0.8310 (ttm) cc_final: 0.7902 (tmt) REVERT: D 598 MET cc_start: 0.3366 (OUTLIER) cc_final: 0.1836 (mtm) REVERT: D 629 MET cc_start: 0.7718 (tmm) cc_final: 0.7300 (tmm) REVERT: D 662 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8145 (ttmm) REVERT: D 784 SER cc_start: 0.8683 (m) cc_final: 0.8390 (p) REVERT: D 824 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 7 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8222 (mp0) REVERT: G 23 GLU cc_start: 0.8536 (tp30) cc_final: 0.8135 (tp30) REVERT: G 26 GLU cc_start: 0.8749 (tp30) cc_final: 0.8294 (tp30) REVERT: G 31 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8367 (mmmm) REVERT: G 36 ASP cc_start: 0.8822 (m-30) cc_final: 0.8533 (m-30) REVERT: C 62 SER cc_start: 0.8551 (p) cc_final: 0.7873 (t) REVERT: C 121 GLU cc_start: 0.9106 (tt0) cc_final: 0.8682 (tt0) REVERT: E 39 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8958 (mm) REVERT: E 70 ASP cc_start: 0.8961 (m-30) cc_final: 0.8653 (p0) REVERT: E 445 MET cc_start: 0.9248 (mmp) cc_final: 0.8924 (mmm) REVERT: E 577 ASP cc_start: 0.3572 (OUTLIER) cc_final: 0.2643 (m-30) REVERT: E 615 MET cc_start: 0.1941 (mmt) cc_final: 0.1202 (mtt) REVERT: E 784 SER cc_start: 0.8678 (m) cc_final: 0.8359 (p) REVERT: E 794 MET cc_start: 0.8985 (ttp) cc_final: 0.8688 (mtm) REVERT: E 798 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (mmt-90) REVERT: E 824 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8901 (tp) REVERT: F 123 GLU cc_start: 0.8988 (tp30) cc_final: 0.8779 (tp30) REVERT: F 559 MET cc_start: 0.5491 (tmt) cc_final: 0.5233 (tmt) REVERT: F 602 MET cc_start: 0.2940 (ptp) cc_final: 0.1694 (mpp) REVERT: F 674 ASN cc_start: 0.9517 (t0) cc_final: 0.9078 (t0) REVERT: F 688 ASP cc_start: 0.9071 (p0) cc_final: 0.8814 (p0) REVERT: F 699 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8172 (mm-30) REVERT: H 16 ILE cc_start: 0.8671 (mt) cc_final: 0.8355 (mp) REVERT: H 17 GLU cc_start: 0.8731 (tp30) cc_final: 0.8158 (tp30) REVERT: H 25 SER cc_start: 0.9072 (p) cc_final: 0.8770 (p) REVERT: H 26 GLU cc_start: 0.8828 (tp30) cc_final: 0.8321 (tp30) REVERT: H 31 LYS cc_start: 0.9042 (mmtp) cc_final: 0.8571 (mmmm) REVERT: H 36 ASP cc_start: 0.8661 (m-30) cc_final: 0.8366 (m-30) REVERT: I 7 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: I 26 GLU cc_start: 0.9018 (tp30) cc_final: 0.8418 (tp30) REVERT: I 31 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8103 (mmmm) REVERT: A 55 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8655 (mt-10) REVERT: A 62 SER cc_start: 0.8746 (p) cc_final: 0.8108 (t) REVERT: B 62 SER cc_start: 0.8682 (p) cc_final: 0.8001 (t) REVERT: B 127 MET cc_start: 0.8362 (ttm) cc_final: 0.8111 (tmm) outliers start: 87 outliers final: 50 residues processed: 493 average time/residue: 0.5674 time to fit residues: 327.5865 Evaluate side-chains 497 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 438 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 662 LYS Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 639 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain F residue 917 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 104 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 308 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 215 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 620 GLN E 545 GLN E 652 GLN F 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.074242 restraints weight = 43144.685| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.44 r_work: 0.2790 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26928 Z= 0.130 Angle : 0.570 11.102 36717 Z= 0.286 Chirality : 0.040 0.173 4371 Planarity : 0.004 0.046 4707 Dihedral : 4.554 56.695 3748 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.35 % Allowed : 18.50 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3.17 (0.14), residues: 3450 helix: 2.80 (0.11), residues: 2187 sheet: 1.51 (0.31), residues: 306 loop : 0.69 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 68 TYR 0.014 0.001 TYR G 76 PHE 0.012 0.001 PHE F 110 TRP 0.009 0.001 TRP C 84 HIS 0.004 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26922) covalent geometry : angle 0.56726 / 0.28 (36705) SS BOND : bond 0.00290 / 0.16 ( 6) SS BOND : angle 2.90915 / 2.01 ( 12) hydrogen bonds : bond 0.04898 / 3.40 ( 1953) hydrogen bonds : angle 4.04271 / 2.93 ( 5682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 461 time to evaluate : 0.861 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: D 178 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7151 (mtp85) REVERT: D 237 MET cc_start: 0.8939 (mtm) cc_final: 0.8511 (mtt) REVERT: D 335 GLN cc_start: 0.8625 (tt0) cc_final: 0.8133 (tm-30) REVERT: D 390 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7257 (tmt-80) REVERT: D 541 MET cc_start: 0.8309 (tpp) cc_final: 0.8027 (tpt) REVERT: D 555 MET cc_start: 0.8300 (ttm) cc_final: 0.7933 (tmt) REVERT: D 629 MET cc_start: 0.7658 (tmm) cc_final: 0.7271 (tmm) REVERT: D 784 SER cc_start: 0.8648 (m) cc_final: 0.8357 (p) REVERT: D 824 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8778 (tp) REVERT: G 7 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8213 (mp0) REVERT: G 23 GLU cc_start: 0.8487 (tp30) cc_final: 0.8000 (tp30) REVERT: G 26 GLU cc_start: 0.8745 (tp30) cc_final: 0.8318 (tp30) REVERT: G 31 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8351 (mmmm) REVERT: G 36 ASP cc_start: 0.8820 (m-30) cc_final: 0.8515 (m-30) REVERT: C 62 SER cc_start: 0.8591 (p) cc_final: 0.7921 (t) REVERT: C 121 GLU cc_start: 0.9132 (tt0) cc_final: 0.8539 (tt0) REVERT: E 70 ASP cc_start: 0.8927 (m-30) cc_final: 0.8643 (p0) REVERT: E 445 MET cc_start: 0.9232 (mmp) cc_final: 0.8884 (mmm) REVERT: E 541 MET cc_start: 0.8198 (tpp) cc_final: 0.7931 (tpp) REVERT: E 577 ASP cc_start: 0.3488 (OUTLIER) cc_final: 0.2616 (m-30) REVERT: E 615 MET cc_start: 0.2084 (mmt) cc_final: 0.1414 (mtt) REVERT: E 794 MET cc_start: 0.8942 (ttp) cc_final: 0.8615 (mtm) REVERT: E 798 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8097 (mmt-90) REVERT: E 824 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (tp) REVERT: F 335 GLN cc_start: 0.8678 (tt0) cc_final: 0.8170 (tm-30) REVERT: F 374 ARG cc_start: 0.7827 (ptt180) cc_final: 0.6987 (ptp-170) REVERT: F 540 GLU cc_start: 0.8773 (tp30) cc_final: 0.8445 (tp30) REVERT: F 602 MET cc_start: 0.2963 (ptp) cc_final: 0.1739 (mpp) REVERT: F 674 ASN cc_start: 0.9508 (t0) cc_final: 0.9065 (t0) REVERT: F 688 ASP cc_start: 0.9005 (p0) cc_final: 0.8761 (p0) REVERT: F 699 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8121 (mm-30) REVERT: H 7 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8444 (mp0) REVERT: H 17 GLU cc_start: 0.8717 (tp30) cc_final: 0.8116 (tp30) REVERT: H 25 SER cc_start: 0.9066 (p) cc_final: 0.8784 (p) REVERT: H 26 GLU cc_start: 0.8787 (tp30) cc_final: 0.8336 (tp30) REVERT: H 30 GLU cc_start: 0.8444 (pm20) cc_final: 0.8187 (pm20) REVERT: H 31 LYS cc_start: 0.9004 (mmtp) cc_final: 0.8632 (mmmm) REVERT: H 36 ASP cc_start: 0.8664 (m-30) cc_final: 0.8396 (m-30) REVERT: H 52 GLU cc_start: 0.8696 (tp30) cc_final: 0.8359 (tp30) REVERT: I 7 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: I 25 SER cc_start: 0.9029 (p) cc_final: 0.8725 (p) REVERT: I 26 GLU cc_start: 0.9017 (tp30) cc_final: 0.8360 (tp30) REVERT: I 31 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8064 (mmmm) REVERT: A 55 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 62 SER cc_start: 0.8792 (p) cc_final: 0.8175 (t) REVERT: B 62 SER cc_start: 0.8666 (p) cc_final: 0.7997 (t) REVERT: B 127 MET cc_start: 0.8297 (ttm) cc_final: 0.8075 (tmm) outliers start: 66 outliers final: 41 residues processed: 498 average time/residue: 0.5998 time to fit residues: 349.0487 Evaluate side-chains 499 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 452 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 253 optimal weight: 0.6980 chunk 266 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 302 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.074136 restraints weight = 43001.043| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.44 r_work: 0.2781 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26928 Z= 0.131 Angle : 0.581 12.729 36717 Z= 0.290 Chirality : 0.041 0.293 4371 Planarity : 0.004 0.051 4707 Dihedral : 4.495 56.778 3747 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.96 % Allowed : 18.96 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3.16 (0.14), residues: 3450 helix: 2.76 (0.11), residues: 2208 sheet: 1.56 (0.31), residues: 306 loop : 0.67 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 68 TYR 0.039 0.001 TYR I 76 PHE 0.011 0.001 PHE F 110 TRP 0.009 0.001 TRP F 835 HIS 0.004 0.000 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (26922) covalent geometry : angle 0.57877 / 0.29 (36705) SS BOND : bond 0.00506 / 0.25 ( 6) SS BOND : angle 2.90501 / 2.02 ( 12) hydrogen bonds : bond 0.04825 / 3.34 ( 1953) hydrogen bonds : angle 4.04361 / 2.93 ( 5682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 475 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ARG cc_start: 0.7377 (mtp85) cc_final: 0.7141 (mtp85) REVERT: D 237 MET cc_start: 0.8931 (mtm) cc_final: 0.8331 (mtt) REVERT: D 335 GLN cc_start: 0.8622 (tt0) cc_final: 0.8130 (tm-30) REVERT: D 373 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.7494 (mppt) REVERT: D 390 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7301 (tmt-80) REVERT: D 541 MET cc_start: 0.8212 (tpp) cc_final: 0.7929 (tpt) REVERT: D 555 MET cc_start: 0.8255 (ttm) cc_final: 0.7996 (tmt) REVERT: D 629 MET cc_start: 0.7696 (tmm) cc_final: 0.7327 (tmm) REVERT: D 784 SER cc_start: 0.8650 (m) cc_final: 0.8367 (p) REVERT: D 824 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8764 (tp) REVERT: G 7 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8216 (mp0) REVERT: G 23 GLU cc_start: 0.8513 (tp30) cc_final: 0.8046 (tp30) REVERT: G 26 GLU cc_start: 0.8735 (tp30) cc_final: 0.8269 (tp30) REVERT: G 31 LYS cc_start: 0.8921 (mmtp) cc_final: 0.8368 (mmmm) REVERT: G 36 ASP cc_start: 0.8851 (m-30) cc_final: 0.8566 (m-30) REVERT: C 23 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7929 (mpp) REVERT: C 62 SER cc_start: 0.8577 (p) cc_final: 0.7919 (t) REVERT: C 121 GLU cc_start: 0.9060 (tt0) cc_final: 0.8568 (tt0) REVERT: E 69 ASN cc_start: 0.9093 (m-40) cc_final: 0.8877 (m-40) REVERT: E 70 ASP cc_start: 0.8931 (m-30) cc_final: 0.8647 (p0) REVERT: E 445 MET cc_start: 0.9189 (mmp) cc_final: 0.8821 (mmm) REVERT: E 541 MET cc_start: 0.8173 (tpp) cc_final: 0.7869 (tpp) REVERT: E 577 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.2639 (m-30) REVERT: E 615 MET cc_start: 0.2123 (mmt) cc_final: 0.1489 (mtt) REVERT: E 784 SER cc_start: 0.8675 (m) cc_final: 0.8364 (p) REVERT: E 794 MET cc_start: 0.8935 (ttp) cc_final: 0.8616 (mtm) REVERT: E 824 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8787 (tp) REVERT: F 207 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8070 (mmmm) REVERT: F 335 GLN cc_start: 0.8677 (tt0) cc_final: 0.8177 (tm-30) REVERT: F 374 ARG cc_start: 0.7692 (ptt180) cc_final: 0.6850 (ptp-170) REVERT: F 602 MET cc_start: 0.2931 (ptp) cc_final: 0.1734 (mpp) REVERT: F 674 ASN cc_start: 0.9527 (t0) cc_final: 0.9090 (t0) REVERT: F 688 ASP cc_start: 0.8992 (p0) cc_final: 0.8745 (p0) REVERT: F 699 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8113 (mm-30) REVERT: H 7 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8473 (mp0) REVERT: H 17 GLU cc_start: 0.8710 (tp30) cc_final: 0.8118 (tp30) REVERT: H 25 SER cc_start: 0.9044 (p) cc_final: 0.8755 (p) REVERT: H 26 GLU cc_start: 0.8795 (tp30) cc_final: 0.8262 (tp30) REVERT: H 31 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8579 (mmmm) REVERT: H 36 ASP cc_start: 0.8615 (m-30) cc_final: 0.8303 (m-30) REVERT: H 52 GLU cc_start: 0.8677 (tp30) cc_final: 0.8411 (tp30) REVERT: I 7 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: I 26 GLU cc_start: 0.9013 (tp30) cc_final: 0.8448 (tp30) REVERT: I 31 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8070 (mmmm) REVERT: A 55 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8655 (mt-10) REVERT: A 62 SER cc_start: 0.8786 (p) cc_final: 0.8192 (t) REVERT: B 62 SER cc_start: 0.8658 (p) cc_final: 0.8002 (t) REVERT: B 127 MET cc_start: 0.8297 (ttm) cc_final: 0.8072 (tmm) outliers start: 55 outliers final: 35 residues processed: 510 average time/residue: 0.6060 time to fit residues: 360.7836 Evaluate side-chains 503 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 461 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 609 ILE Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 4 THR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 138 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070713 restraints weight = 43373.910| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.46 r_work: 0.2721 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26928 Z= 0.221 Angle : 0.635 11.636 36717 Z= 0.322 Chirality : 0.043 0.299 4371 Planarity : 0.004 0.042 4707 Dihedral : 4.568 57.151 3743 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.45 % Allowed : 18.85 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.98 (0.14), residues: 3450 helix: 2.61 (0.11), residues: 2193 sheet: 1.46 (0.30), residues: 330 loop : 0.67 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 628 TYR 0.017 0.001 TYR F 776 PHE 0.013 0.001 PHE D 703 TRP 0.010 0.001 TRP E 381 HIS 0.004 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (26922) covalent geometry : angle 0.63133 / 0.32 (36705) SS BOND : bond 0.00362 / 0.22 ( 6) SS BOND : angle 3.90303 / 2.57 ( 12) hydrogen bonds : bond 0.05724 / 3.95 ( 1953) hydrogen bonds : angle 4.18851 / 3.03 ( 5682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11394.68 seconds wall clock time: 193 minutes 47.65 seconds (11627.65 seconds total)