Starting phenix.real_space_refine on Sat Aug 8 07:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vn9_65204/08_2026/9vn9_65204.map" } resolution = 3.48 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= 0.008 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 12 5.49 5 S 116 5.16 5 C 17084 2.51 5 N 4288 2.21 5 O 4740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s 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: 26240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6513 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 15, 'TRANS': 792} Chain breaks: 15 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6513 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 15, 'TRANS': 792} Chain breaks: 15 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6513 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 15, 'TRANS': 792} Chain breaks: 15 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6513 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 15, 'TRANS': 792} Chain breaks: 15 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.21 Number of scatterers: 26240 At special positions: 0 Unit cell: (126.824, 126.824, 141.432, 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 116 16.00 P 12 15.00 O 4740 8.00 N 4288 7.00 C 17084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 822.3 milliseconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 8 sheets defined 76.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.681A pdb=" N LYS A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 437 removed outlier: 4.082A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 454 through 468 removed outlier: 5.103A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 498 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.638A pdb=" N THR A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 607 through 636 Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 733 through 757 Processing helix chain 'A' and resid 765 through 788 removed outlier: 4.262A pdb=" N MET A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 796 through 818 Processing helix chain 'A' and resid 821 through 844 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 867 removed outlier: 4.120A pdb=" N ILE A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 889 removed outlier: 3.984A pdb=" N PHE A 874 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 876 " --> pdb=" O PHE A 872 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 912 Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 956 through 988 Processing helix chain 'A' and resid 990 through 1008 removed outlier: 3.598A pdb=" N TRP A 994 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1072 Processing helix chain 'A' and resid 1075 through 1104 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.664A pdb=" N LYS B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 425 through 437 removed outlier: 4.082A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 454 through 468 removed outlier: 5.123A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 498 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.731A pdb=" N LYS B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 529 " --> pdb=" O TRP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 574 through 584 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 607 through 636 Processing helix chain 'B' and resid 637 through 646 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 733 through 757 Processing helix chain 'B' and resid 765 through 788 removed outlier: 4.250A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 796 through 818 Processing helix chain 'B' and resid 821 through 844 Processing helix chain 'B' and resid 845 through 850 Processing helix chain 'B' and resid 853 through 867 removed outlier: 3.899A pdb=" N ILE B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 889 removed outlier: 3.940A pdb=" N PHE B 874 " --> pdb=" O PHE B 870 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 876 " --> pdb=" O PHE B 872 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 883 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 888 " --> pdb=" O ALA B 884 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 889 " --> pdb=" O ARG B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 912 Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 956 through 988 Processing helix chain 'B' and resid 990 through 1008 removed outlier: 3.580A pdb=" N TRP B 994 " --> pdb=" O ASN B 990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1072 Processing helix chain 'B' and resid 1075 through 1104 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.696A pdb=" N LYS C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 Processing helix chain 'C' and resid 403 through 419 Processing helix chain 'C' and resid 425 through 437 removed outlier: 4.081A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 454 through 468 removed outlier: 5.126A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 498 Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 520 through 532 removed outlier: 3.727A pdb=" N LYS C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 529 " --> pdb=" O TRP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 607 through 636 Processing helix chain 'C' and resid 637 through 646 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 733 through 757 Processing helix chain 'C' and resid 765 through 788 removed outlier: 4.246A pdb=" N MET C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 796 Processing helix chain 'C' and resid 796 through 818 Processing helix chain 'C' and resid 821 through 844 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 853 through 867 removed outlier: 3.894A pdb=" N ILE C 857 " --> pdb=" O LEU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 889 removed outlier: 3.955A pdb=" N PHE C 874 " --> pdb=" O PHE C 870 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 883 " --> pdb=" O VAL C 879 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 889 " --> pdb=" O ARG C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 912 Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 956 through 988 Processing helix chain 'C' and resid 990 through 1008 removed outlier: 3.580A pdb=" N TRP C 994 " --> pdb=" O ASN C 990 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1072 Processing helix chain 'C' and resid 1075 through 1104 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.704A pdb=" N LYS D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 425 through 437 removed outlier: 4.082A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 454 through 468 removed outlier: 5.122A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 498 Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.648A pdb=" N THR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 529 " --> pdb=" O TRP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 586 through 603 Processing helix chain 'D' and resid 607 through 636 Processing helix chain 'D' and resid 637 through 646 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 733 through 757 Processing helix chain 'D' and resid 765 through 788 removed outlier: 4.255A pdb=" N MET D 788 " --> pdb=" O ARG D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 796 Processing helix chain 'D' and resid 796 through 818 Processing helix chain 'D' and resid 821 through 844 Processing helix chain 'D' and resid 845 through 850 Processing helix chain 'D' and resid 853 through 867 removed outlier: 3.897A pdb=" N ILE D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 889 removed outlier: 3.960A pdb=" N PHE D 874 " --> pdb=" O PHE D 870 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 876 " --> pdb=" O PHE D 872 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP D 877 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 883 " --> pdb=" O VAL D 879 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 888 " --> pdb=" O ALA D 884 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 889 " --> pdb=" O ARG D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 912 Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 956 through 988 Processing helix chain 'D' and resid 990 through 1008 removed outlier: 3.582A pdb=" N TRP D 994 " --> pdb=" O ASN D 990 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1072 Processing helix chain 'D' and resid 1075 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.594A pdb=" N LEU A 118 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 removed outlier: 6.181A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 145 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 119 removed outlier: 6.593A pdb=" N LEU B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 212 through 213 removed outlier: 6.183A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 145 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'C' and resid 212 through 213 removed outlier: 6.290A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 145 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 removed outlier: 6.577A pdb=" N LEU D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 212 through 213 removed outlier: 6.281A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 145 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) 1766 hydrogen bonds defined for protein. 5262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4188 1.31 - 1.43: 7474 1.43 - 1.56: 14930 1.56 - 1.68: 16 1.68 - 1.81: 184 Bond restraints: 26792 Sorted by residual: bond pdb=" C1B PIO D1201 " pdb=" O3C PIO D1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1B PIO B1201 " pdb=" O3C PIO B1201 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1B PIO C1201 " pdb=" O3C PIO C1201 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1A PIO D1201 " pdb=" O2C PIO D1201 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 26787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 35816 2.30 - 4.61: 398 4.61 - 6.91: 61 6.91 - 9.22: 13 9.22 - 11.52: 12 Bond angle restraints: 36300 Sorted by residual: angle pdb=" O11 PIO A1201 " pdb=" P1 PIO A1201 " pdb=" O12 PIO A1201 " ideal model delta sigma weight residual 121.09 109.57 11.52 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O11 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O12 PIO D1201 " ideal model delta sigma weight residual 121.09 109.58 11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O11 PIO B1201 " pdb=" P1 PIO B1201 " pdb=" O12 PIO B1201 " ideal model delta sigma weight residual 121.09 109.60 11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O11 PIO C1201 " pdb=" P1 PIO C1201 " pdb=" O12 PIO C1201 " ideal model delta sigma weight residual 121.09 109.60 11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O1 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O13 PIO D1201 " ideal model delta sigma weight residual 97.64 109.08 -11.44 3.00e+00 1.11e-01 1.46e+01 ... (remaining 36295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13589 17.85 - 35.69: 1574 35.69 - 53.54: 346 53.54 - 71.38: 125 71.38 - 89.23: 18 Dihedral angle restraints: 15652 sinusoidal: 6164 harmonic: 9488 Sorted by residual: dihedral pdb=" CA ASN A 572 " pdb=" C ASN A 572 " pdb=" N LYS A 573 " pdb=" CA LYS A 573 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 337 " pdb=" CB ASP A 337 " pdb=" CG ASP A 337 " pdb=" OD1 ASP A 337 " ideal model delta sinusoidal sigma weight residual -30.00 -85.99 55.99 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASN D 572 " pdb=" C ASN D 572 " pdb=" N LYS D 573 " pdb=" CA LYS D 573 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 15649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3300 0.036 - 0.073: 602 0.073 - 0.109: 214 0.109 - 0.146: 32 0.146 - 0.182: 4 Chirality restraints: 4152 Sorted by residual: chirality pdb=" CB THR D 967 " pdb=" CA THR D 967 " pdb=" OG1 THR D 967 " pdb=" CG2 THR D 967 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB THR C 967 " pdb=" CA THR C 967 " pdb=" OG1 THR C 967 " pdb=" CG2 THR C 967 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB THR B 967 " pdb=" CA THR B 967 " pdb=" OG1 THR B 967 " pdb=" CG2 THR B 967 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 4149 not shown) Planarity restraints: 4456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 623 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C THR A 623 " 0.044 2.00e-02 2.50e+03 pdb=" O THR A 623 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 624 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 623 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C THR C 623 " -0.044 2.00e-02 2.50e+03 pdb=" O THR C 623 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG C 624 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 623 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C THR D 623 " -0.044 2.00e-02 2.50e+03 pdb=" O THR D 623 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG D 624 " 0.015 2.00e-02 2.50e+03 ... (remaining 4453 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7280 2.81 - 3.34: 27852 3.34 - 3.86: 42569 3.86 - 4.38: 46293 4.38 - 4.90: 79821 Nonbonded interactions: 203815 Sorted by model distance: nonbonded pdb=" O ASN D 572 " pdb=" ND2 ASN D 572 " model vdw 2.292 3.120 nonbonded pdb=" O ASN A 572 " pdb=" ND2 ASN A 572 " model vdw 2.331 3.120 nonbonded pdb=" O THR D 623 " pdb=" OE1 GLU D 627 " model vdw 2.373 3.040 nonbonded pdb=" O THR C 623 " pdb=" OE1 GLU C 627 " model vdw 2.374 3.040 nonbonded pdb=" O THR A 623 " pdb=" OE1 GLU A 627 " model vdw 2.376 3.040 ... (remaining 203810 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Normalize map: mean=0, sd=1: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.690 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.003 0.068 26792 Z= 0.168 Angle : 0.645 11.523 36300 Z= 0.327 Chirality : 0.034 0.182 4152 Planarity : 0.004 0.041 4456 Dihedral : 16.601 89.231 9460 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.08 % Allowed : 13.60 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3104 helix: 1.88 (0.10), residues: 2396 sheet: -3.09 (0.44), residues: 120 loop : -1.81 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 197 TYR 0.013 0.001 TYR A 999 PHE 0.022 0.001 PHE A 869 TRP 0.021 0.001 TRP C 380 HIS 0.006 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (26792) covalent geometry : angle 0.64479 / 0.33 (36300) hydrogen bonds : bond 0.10459 / 7.09 ( 1766) hydrogen bonds : angle 4.94043 / 3.51 ( 5262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6894 (tptt) cc_final: 0.6391 (tttt) REVERT: A 395 LYS cc_start: 0.7962 (tttt) cc_final: 0.7708 (pptt) REVERT: A 801 MET cc_start: 0.4570 (mmm) cc_final: 0.3426 (ptm) REVERT: B 116 LYS cc_start: 0.6931 (tptt) cc_final: 0.6422 (tttt) REVERT: B 395 LYS cc_start: 0.7904 (tttt) cc_final: 0.7640 (pptt) REVERT: B 801 MET cc_start: 0.3577 (mtm) cc_final: 0.3260 (ptm) REVERT: C 116 LYS cc_start: 0.6919 (tptt) cc_final: 0.6382 (tttt) REVERT: C 395 LYS cc_start: 0.7905 (tttt) cc_final: 0.7643 (pptt) REVERT: C 601 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7901 (mp) REVERT: C 801 MET cc_start: 0.3544 (mtm) cc_final: 0.3245 (ptm) REVERT: D 106 ILE cc_start: 0.6594 (mt) cc_final: 0.6050 (mt) REVERT: D 116 LYS cc_start: 0.6955 (tptt) cc_final: 0.6382 (tttt) REVERT: D 382 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7860 (mmtt) REVERT: D 395 LYS cc_start: 0.7959 (tttt) cc_final: 0.7603 (pptt) REVERT: D 452 ARG cc_start: 0.7606 (tpt90) cc_final: 0.7111 (tmt-80) REVERT: D 601 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 801 MET cc_start: 0.3586 (mtm) cc_final: 0.3288 (ptm) REVERT: D 862 ARG cc_start: 0.7323 (mmt180) cc_final: 0.7111 (mmt180) outliers start: 30 outliers final: 21 residues processed: 346 average time/residue: 0.1690 time to fit residues: 93.0446 Evaluate side-chains 327 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 869 PHE Chi-restraints excluded: chain D residue 871 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 30.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 973 ASN B 138 HIS B 973 ASN C 138 HIS C 973 ASN D 138 HIS D 572 ASN ** D 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.210737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.174277 restraints weight = 36205.146| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.69 r_work: 0.3874 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26792 Z= 0.185 Angle : 0.581 8.404 36300 Z= 0.311 Chirality : 0.039 0.198 4152 Planarity : 0.004 0.040 4456 Dihedral : 6.658 63.309 3535 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.19 % Allowed : 13.63 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.15), residues: 3104 helix: 1.92 (0.10), residues: 2400 sheet: -2.98 (0.44), residues: 124 loop : -1.96 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.014 0.001 TYR A 999 PHE 0.027 0.002 PHE D 738 TRP 0.016 0.001 TRP B 994 HIS 0.006 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (26792) covalent geometry : angle 0.58115 / 0.31 (36300) hydrogen bonds : bond 0.05428 / 3.66 ( 1766) hydrogen bonds : angle 4.25711 / 3.03 ( 5262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.7065 (tptt) cc_final: 0.6487 (tttt) REVERT: A 395 LYS cc_start: 0.8053 (tttt) cc_final: 0.7767 (pptt) REVERT: A 623 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7427 (t) REVERT: A 801 MET cc_start: 0.4436 (mmm) cc_final: 0.3812 (ptm) REVERT: A 862 ARG cc_start: 0.7237 (mmt180) cc_final: 0.6475 (mtm180) REVERT: A 863 MET cc_start: 0.8120 (tmm) cc_final: 0.7873 (tmm) REVERT: B 116 LYS cc_start: 0.7123 (tptt) cc_final: 0.6504 (tttt) REVERT: B 395 LYS cc_start: 0.8022 (tttt) cc_final: 0.7717 (pptt) REVERT: B 801 MET cc_start: 0.3859 (mtm) cc_final: 0.3548 (ptm) REVERT: B 862 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6576 (mtm180) REVERT: C 116 LYS cc_start: 0.7054 (tptt) cc_final: 0.6485 (tttt) REVERT: C 395 LYS cc_start: 0.7933 (tttt) cc_final: 0.7716 (pptt) REVERT: C 601 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8026 (mp) REVERT: C 623 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7452 (t) REVERT: C 801 MET cc_start: 0.3841 (mtm) cc_final: 0.3512 (ptm) REVERT: C 862 ARG cc_start: 0.7318 (mmt180) cc_final: 0.6588 (mtm180) REVERT: D 116 LYS cc_start: 0.6988 (tptt) cc_final: 0.6400 (tttt) REVERT: D 382 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7879 (mmtt) REVERT: D 395 LYS cc_start: 0.7988 (tttt) cc_final: 0.7703 (pptt) REVERT: D 601 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (mp) REVERT: D 623 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7444 (t) REVERT: D 801 MET cc_start: 0.3817 (mtm) cc_final: 0.3509 (ptm) REVERT: D 862 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6603 (mtm180) outliers start: 61 outliers final: 29 residues processed: 364 average time/residue: 0.1654 time to fit residues: 95.6391 Evaluate side-chains 308 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 847 PHE Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 857 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 294 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 138 HIS D 572 ASN D 973 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.213653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175314 restraints weight = 36544.797| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.54 r_work: 0.3933 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26792 Z= 0.125 Angle : 0.507 7.957 36300 Z= 0.274 Chirality : 0.036 0.189 4152 Planarity : 0.003 0.044 4456 Dihedral : 6.055 63.884 3501 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.16 % Allowed : 14.82 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.15), residues: 3104 helix: 2.10 (0.10), residues: 2396 sheet: -2.62 (0.47), residues: 124 loop : -1.97 (0.20), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 119 TYR 0.016 0.001 TYR A 999 PHE 0.019 0.001 PHE B 881 TRP 0.019 0.001 TRP B 994 HIS 0.007 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (26792) covalent geometry : angle 0.50679 / 0.27 (36300) hydrogen bonds : bond 0.04522 / 3.05 ( 1766) hydrogen bonds : angle 4.03825 / 2.88 ( 5262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6791 (tptt) cc_final: 0.6226 (ttpt) REVERT: A 395 LYS cc_start: 0.8036 (tttt) cc_final: 0.7698 (pptt) REVERT: A 801 MET cc_start: 0.4563 (mmm) cc_final: 0.4104 (ptm) REVERT: A 862 ARG cc_start: 0.7081 (mmt180) cc_final: 0.6398 (mtm180) REVERT: B 116 LYS cc_start: 0.6817 (tptt) cc_final: 0.6232 (ttpt) REVERT: B 395 LYS cc_start: 0.7997 (tttt) cc_final: 0.7634 (pptt) REVERT: B 801 MET cc_start: 0.3990 (mtm) cc_final: 0.3632 (ptm) REVERT: B 862 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6511 (mtm180) REVERT: C 116 LYS cc_start: 0.6824 (tptt) cc_final: 0.6247 (ttpt) REVERT: C 395 LYS cc_start: 0.7952 (tttt) cc_final: 0.7632 (pptt) REVERT: C 801 MET cc_start: 0.4019 (mtm) cc_final: 0.3640 (ptm) REVERT: C 862 ARG cc_start: 0.7192 (mmt180) cc_final: 0.6592 (mtm180) REVERT: D 116 LYS cc_start: 0.6899 (tptt) cc_final: 0.6301 (tttt) REVERT: D 382 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7933 (mmtt) REVERT: D 395 LYS cc_start: 0.7989 (tttt) cc_final: 0.7633 (pptt) REVERT: D 452 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7206 (tmt-80) REVERT: D 801 MET cc_start: 0.3959 (mtm) cc_final: 0.3604 (ptm) REVERT: D 862 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6609 (mtm180) outliers start: 60 outliers final: 36 residues processed: 359 average time/residue: 0.1650 time to fit residues: 95.1441 Evaluate side-chains 312 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 847 PHE Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.213318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.174814 restraints weight = 35261.260| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.26 r_work: 0.3976 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26792 Z= 0.182 Angle : 0.597 10.588 36300 Z= 0.315 Chirality : 0.039 0.183 4152 Planarity : 0.004 0.039 4456 Dihedral : 6.111 67.890 3497 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.23 % Allowed : 15.61 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 3104 helix: 1.99 (0.10), residues: 2396 sheet: -2.65 (0.47), residues: 124 loop : -2.00 (0.20), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 452 TYR 0.013 0.001 TYR D 999 PHE 0.024 0.002 PHE D 738 TRP 0.014 0.001 TRP B 994 HIS 0.012 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (26792) covalent geometry : angle 0.59748 / 0.31 (36300) hydrogen bonds : bond 0.05244 / 3.53 ( 1766) hydrogen bonds : angle 4.16850 / 2.96 ( 5262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6966 (tptt) cc_final: 0.6358 (tttt) REVERT: A 631 GLU cc_start: 0.8094 (tp30) cc_final: 0.7860 (tm-30) REVERT: A 765 HIS cc_start: 0.3537 (t-170) cc_final: 0.3309 (t-170) REVERT: A 801 MET cc_start: 0.4466 (mmm) cc_final: 0.4114 (ptm) REVERT: B 116 LYS cc_start: 0.6997 (tptt) cc_final: 0.6335 (ttpt) REVERT: B 356 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8367 (pp20) REVERT: B 395 LYS cc_start: 0.7909 (tttt) cc_final: 0.7700 (pptt) REVERT: B 526 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8145 (mtmt) REVERT: B 801 MET cc_start: 0.4057 (mtm) cc_final: 0.3704 (ptm) REVERT: B 862 ARG cc_start: 0.7230 (mmt180) cc_final: 0.6707 (mtm180) REVERT: C 116 LYS cc_start: 0.6938 (tptt) cc_final: 0.6378 (tttt) REVERT: C 526 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: C 601 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8087 (mp) REVERT: C 801 MET cc_start: 0.3952 (mtm) cc_final: 0.3595 (ptm) REVERT: C 862 ARG cc_start: 0.7242 (mmt180) cc_final: 0.6711 (mtm180) REVERT: D 116 LYS cc_start: 0.7032 (tptt) cc_final: 0.6432 (tttt) REVERT: D 452 ARG cc_start: 0.7495 (tpt90) cc_final: 0.7006 (tmt-80) REVERT: D 601 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 801 MET cc_start: 0.4077 (mtm) cc_final: 0.3713 (ptm) REVERT: D 862 ARG cc_start: 0.7251 (mmt180) cc_final: 0.6734 (mtm180) outliers start: 62 outliers final: 40 residues processed: 342 average time/residue: 0.1754 time to fit residues: 95.6970 Evaluate side-chains 320 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 307 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.218135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.179419 restraints weight = 35801.354| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.16 r_work: 0.4058 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26792 Z= 0.114 Angle : 0.510 12.316 36300 Z= 0.271 Chirality : 0.036 0.167 4152 Planarity : 0.003 0.047 4456 Dihedral : 5.717 68.431 3496 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.01 % Allowed : 16.55 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3104 helix: 2.20 (0.10), residues: 2392 sheet: -2.11 (0.49), residues: 124 loop : -2.00 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 452 TYR 0.017 0.001 TYR A 999 PHE 0.019 0.001 PHE B 881 TRP 0.021 0.001 TRP B 994 HIS 0.006 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (26792) covalent geometry : angle 0.51047 / 0.27 (36300) hydrogen bonds : bond 0.04075 / 2.74 ( 1766) hydrogen bonds : angle 3.95329 / 2.82 ( 5262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.5882 (mt) REVERT: A 116 LYS cc_start: 0.6717 (tptt) cc_final: 0.6198 (ttpt) REVERT: A 735 PHE cc_start: 0.7380 (t80) cc_final: 0.7116 (t80) REVERT: A 801 MET cc_start: 0.4470 (mmm) cc_final: 0.4263 (ptm) REVERT: A 862 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6554 (mtm180) REVERT: A 863 MET cc_start: 0.8260 (tmm) cc_final: 0.7934 (tmm) REVERT: A 981 TYR cc_start: 0.7131 (t80) cc_final: 0.6597 (t80) REVERT: B 106 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.5897 (mt) REVERT: B 116 LYS cc_start: 0.6733 (tptt) cc_final: 0.6171 (ttpt) REVERT: B 209 ILE cc_start: 0.7876 (tp) cc_final: 0.7532 (tt) REVERT: B 395 LYS cc_start: 0.7919 (tttt) cc_final: 0.7662 (pptt) REVERT: B 801 MET cc_start: 0.4073 (mtm) cc_final: 0.3715 (ptm) REVERT: B 862 ARG cc_start: 0.7213 (mmt180) cc_final: 0.6719 (mtm180) REVERT: B 981 TYR cc_start: 0.7124 (t80) cc_final: 0.6644 (t80) REVERT: C 106 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.5782 (mt) REVERT: C 116 LYS cc_start: 0.6707 (tptt) cc_final: 0.6209 (ttpt) REVERT: C 391 LEU cc_start: 0.9170 (tt) cc_final: 0.8915 (tp) REVERT: C 801 MET cc_start: 0.4073 (mtm) cc_final: 0.3709 (ptm) REVERT: C 862 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6643 (mtm180) REVERT: D 116 LYS cc_start: 0.6822 (tptt) cc_final: 0.6280 (tttt) REVERT: D 209 ILE cc_start: 0.7815 (tp) cc_final: 0.7449 (tt) REVERT: D 452 ARG cc_start: 0.7355 (tpt90) cc_final: 0.6829 (tmt-80) REVERT: D 801 MET cc_start: 0.4084 (mtm) cc_final: 0.3716 (ptm) REVERT: D 862 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6660 (mtm180) outliers start: 56 outliers final: 37 residues processed: 354 average time/residue: 0.1716 time to fit residues: 95.8521 Evaluate side-chains 323 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 1006 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 187 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 248 optimal weight: 0.0670 chunk 109 optimal weight: 6.9990 chunk 268 optimal weight: 0.0040 chunk 144 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 overall best weight: 0.9932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.218331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.179795 restraints weight = 35842.684| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.25 r_work: 0.4025 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26792 Z= 0.113 Angle : 0.506 9.902 36300 Z= 0.271 Chirality : 0.036 0.221 4152 Planarity : 0.003 0.047 4456 Dihedral : 5.552 68.954 3496 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.94 % Allowed : 16.69 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.15), residues: 3104 helix: 2.22 (0.10), residues: 2392 sheet: -2.21 (0.54), residues: 100 loop : -2.07 (0.19), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 624 TYR 0.016 0.001 TYR C 999 PHE 0.027 0.001 PHE B 752 TRP 0.019 0.001 TRP B 994 HIS 0.010 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (26792) covalent geometry : angle 0.50581 / 0.27 (36300) hydrogen bonds : bond 0.04003 / 2.71 ( 1766) hydrogen bonds : angle 3.91833 / 2.79 ( 5262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6756 (tptt) cc_final: 0.6206 (ttpt) REVERT: A 862 ARG cc_start: 0.7200 (mmt180) cc_final: 0.6598 (mtm180) REVERT: A 863 MET cc_start: 0.8203 (tmm) cc_final: 0.7952 (tmm) REVERT: A 886 GLN cc_start: 0.4735 (mm-40) cc_final: 0.4368 (mm-40) REVERT: A 981 TYR cc_start: 0.7142 (t80) cc_final: 0.6616 (t80) REVERT: B 116 LYS cc_start: 0.6743 (tptt) cc_final: 0.6199 (ttpt) REVERT: B 209 ILE cc_start: 0.7918 (tp) cc_final: 0.7591 (tt) REVERT: B 395 LYS cc_start: 0.7927 (tttt) cc_final: 0.7661 (pptt) REVERT: B 801 MET cc_start: 0.4082 (mtm) cc_final: 0.3702 (ptm) REVERT: B 862 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6675 (mtm180) REVERT: B 981 TYR cc_start: 0.7143 (t80) cc_final: 0.6637 (t80) REVERT: C 106 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.5553 (mt) REVERT: C 116 LYS cc_start: 0.6775 (tptt) cc_final: 0.6196 (tttt) REVERT: C 391 LEU cc_start: 0.9195 (tt) cc_final: 0.8930 (tp) REVERT: C 801 MET cc_start: 0.4053 (mtm) cc_final: 0.3694 (ptm) REVERT: C 862 ARG cc_start: 0.7212 (mmt180) cc_final: 0.6674 (mtm180) REVERT: C 981 TYR cc_start: 0.7173 (t80) cc_final: 0.6695 (t80) REVERT: C 1059 MET cc_start: 0.7575 (mmm) cc_final: 0.7255 (mpp) REVERT: D 116 LYS cc_start: 0.6883 (tptt) cc_final: 0.6325 (tttt) REVERT: D 209 ILE cc_start: 0.7859 (tp) cc_final: 0.7498 (tt) REVERT: D 452 ARG cc_start: 0.7325 (tpt90) cc_final: 0.6857 (tmt-80) REVERT: D 801 MET cc_start: 0.4066 (mtm) cc_final: 0.3709 (ptm) REVERT: D 862 ARG cc_start: 0.7244 (mmt180) cc_final: 0.6673 (mtm180) REVERT: D 1059 MET cc_start: 0.7552 (mmm) cc_final: 0.7237 (mpp) outliers start: 54 outliers final: 42 residues processed: 347 average time/residue: 0.1618 time to fit residues: 90.3835 Evaluate side-chains 320 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 1006 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 220 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN D 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.209602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.173878 restraints weight = 35662.240| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.34 r_work: 0.3915 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 26792 Z= 0.290 Angle : 0.709 10.486 36300 Z= 0.373 Chirality : 0.042 0.268 4152 Planarity : 0.004 0.045 4456 Dihedral : 6.232 78.388 3496 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.66 % Allowed : 16.91 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3104 helix: 1.71 (0.10), residues: 2396 sheet: -2.83 (0.52), residues: 100 loop : -2.30 (0.19), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 688 TYR 0.018 0.002 TYR C 240 PHE 0.033 0.003 PHE B 738 TRP 0.015 0.002 TRP A 581 HIS 0.011 0.002 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.29 (26792) covalent geometry : angle 0.70923 / 0.37 (36300) hydrogen bonds : bond 0.06093 / 4.11 ( 1766) hydrogen bonds : angle 4.41457 / 3.14 ( 5262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.5996 (mt) REVERT: A 116 LYS cc_start: 0.7123 (tptt) cc_final: 0.6572 (tttt) REVERT: A 638 ASP cc_start: 0.7816 (t0) cc_final: 0.7614 (t0) REVERT: A 865 ILE cc_start: 0.6539 (mt) cc_final: 0.6278 (mm) REVERT: B 106 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.5994 (mt) REVERT: B 116 LYS cc_start: 0.7117 (tptt) cc_final: 0.6553 (tttt) REVERT: B 981 TYR cc_start: 0.7091 (t80) cc_final: 0.6467 (t80) REVERT: C 106 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6031 (mt) REVERT: C 116 LYS cc_start: 0.7027 (tptt) cc_final: 0.6474 (tttt) REVERT: C 981 TYR cc_start: 0.7079 (t80) cc_final: 0.6469 (t80) REVERT: D 116 LYS cc_start: 0.7154 (tptt) cc_final: 0.6551 (tttt) REVERT: D 452 ARG cc_start: 0.7417 (tpt90) cc_final: 0.6942 (tmt-80) outliers start: 74 outliers final: 46 residues processed: 331 average time/residue: 0.1688 time to fit residues: 90.9691 Evaluate side-chains 318 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 7 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 305 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 ASN D 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.217533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.178907 restraints weight = 35793.062| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.22 r_work: 0.4045 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 26792 Z= 0.118 Angle : 0.536 10.040 36300 Z= 0.286 Chirality : 0.037 0.170 4152 Planarity : 0.003 0.049 4456 Dihedral : 5.810 79.386 3496 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.19 % Allowed : 19.35 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 3104 helix: 2.04 (0.10), residues: 2388 sheet: -2.50 (0.54), residues: 100 loop : -2.07 (0.19), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 475 TYR 0.016 0.001 TYR C 999 PHE 0.018 0.001 PHE B 881 TRP 0.026 0.001 TRP B 994 HIS 0.017 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (26792) covalent geometry : angle 0.53630 / 0.29 (36300) hydrogen bonds : bond 0.04107 / 2.75 ( 1766) hydrogen bonds : angle 4.05680 / 2.90 ( 5262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6673 (tptt) cc_final: 0.6198 (ttpt) REVERT: A 631 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 862 ARG cc_start: 0.7215 (mmt180) cc_final: 0.6609 (mtm180) REVERT: A 865 ILE cc_start: 0.6390 (mt) cc_final: 0.6166 (mm) REVERT: A 878 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5408 (mtt) REVERT: B 116 LYS cc_start: 0.6671 (tptt) cc_final: 0.6192 (ttpt) REVERT: B 801 MET cc_start: 0.4107 (mtm) cc_final: 0.3740 (ptm) REVERT: B 862 ARG cc_start: 0.7226 (mmt180) cc_final: 0.6709 (mtm180) REVERT: B 981 TYR cc_start: 0.7095 (t80) cc_final: 0.6511 (t80) REVERT: C 116 LYS cc_start: 0.6738 (tptt) cc_final: 0.6239 (tttt) REVERT: C 189 MET cc_start: 0.7487 (mtt) cc_final: 0.7078 (mmm) REVERT: C 801 MET cc_start: 0.4135 (mtm) cc_final: 0.3575 (ptm) REVERT: C 862 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6668 (mtm180) REVERT: D 116 LYS cc_start: 0.6696 (tptt) cc_final: 0.6198 (tttt) REVERT: D 452 ARG cc_start: 0.7283 (tpt90) cc_final: 0.6896 (tmt-80) REVERT: D 801 MET cc_start: 0.4148 (mtm) cc_final: 0.3752 (ptm) REVERT: D 862 ARG cc_start: 0.7224 (mmt180) cc_final: 0.6684 (mtm180) REVERT: D 981 TYR cc_start: 0.7122 (t80) cc_final: 0.6612 (t80) outliers start: 33 outliers final: 27 residues processed: 316 average time/residue: 0.1712 time to fit residues: 87.5838 Evaluate side-chains 297 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 121 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 269 optimal weight: 0.7980 chunk 168 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 248 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.219429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.182024 restraints weight = 36277.155| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.13 r_work: 0.4075 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26792 Z= 0.110 Angle : 0.517 10.413 36300 Z= 0.274 Chirality : 0.037 0.204 4152 Planarity : 0.003 0.048 4456 Dihedral : 5.488 81.103 3496 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.19 % Allowed : 19.89 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.15), residues: 3104 helix: 2.18 (0.10), residues: 2384 sheet: -1.77 (0.48), residues: 124 loop : -2.01 (0.20), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 452 TYR 0.018 0.001 TYR B 999 PHE 0.021 0.001 PHE A 752 TRP 0.024 0.001 TRP B 994 HIS 0.013 0.001 HIS D 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (26792) covalent geometry : angle 0.51699 / 0.27 (36300) hydrogen bonds : bond 0.03773 / 2.54 ( 1766) hydrogen bonds : angle 3.94916 / 2.82 ( 5262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6768 (tptt) cc_final: 0.6204 (tttt) REVERT: A 862 ARG cc_start: 0.7273 (mmt180) cc_final: 0.6669 (mtm180) REVERT: A 865 ILE cc_start: 0.6425 (mt) cc_final: 0.6205 (mm) REVERT: A 878 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5383 (mtt) REVERT: B 116 LYS cc_start: 0.6756 (tptt) cc_final: 0.6194 (tttt) REVERT: B 801 MET cc_start: 0.4135 (mtm) cc_final: 0.3773 (ptm) REVERT: B 862 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6744 (mtm180) REVERT: B 981 TYR cc_start: 0.7012 (t80) cc_final: 0.6424 (t80) REVERT: C 116 LYS cc_start: 0.6675 (tptt) cc_final: 0.6152 (tttt) REVERT: C 189 MET cc_start: 0.7527 (mtt) cc_final: 0.7127 (mmm) REVERT: C 781 ASP cc_start: 0.4212 (t0) cc_final: 0.3736 (m-30) REVERT: C 801 MET cc_start: 0.4169 (mtm) cc_final: 0.3640 (ptm) REVERT: C 862 ARG cc_start: 0.7230 (mmt180) cc_final: 0.6702 (mtm180) REVERT: D 116 LYS cc_start: 0.6644 (tptt) cc_final: 0.6142 (tttt) REVERT: D 452 ARG cc_start: 0.7212 (tpt90) cc_final: 0.6848 (tmt-80) REVERT: D 781 ASP cc_start: 0.4139 (t0) cc_final: 0.3696 (m-30) REVERT: D 801 MET cc_start: 0.4124 (mtm) cc_final: 0.3750 (ptm) REVERT: D 862 ARG cc_start: 0.7263 (mmt180) cc_final: 0.6660 (mtm180) outliers start: 33 outliers final: 28 residues processed: 320 average time/residue: 0.1763 time to fit residues: 91.4699 Evaluate side-chains 305 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 122 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.0060 chunk 88 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.218814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.181578 restraints weight = 36302.984| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.21 r_work: 0.4064 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26792 Z= 0.114 Angle : 0.540 12.563 36300 Z= 0.283 Chirality : 0.037 0.200 4152 Planarity : 0.003 0.048 4456 Dihedral : 5.355 82.199 3493 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.04 % Allowed : 20.14 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.15), residues: 3104 helix: 2.16 (0.10), residues: 2384 sheet: -2.12 (0.54), residues: 100 loop : -2.01 (0.19), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 842 TYR 0.016 0.001 TYR A 999 PHE 0.024 0.001 PHE B 752 TRP 0.023 0.001 TRP B 994 HIS 0.016 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (26792) covalent geometry : angle 0.53956 / 0.28 (36300) hydrogen bonds : bond 0.03818 / 2.58 ( 1766) hydrogen bonds : angle 3.96751 / 2.83 ( 5262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.6801 (tptt) cc_final: 0.6262 (tttt) REVERT: A 862 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6754 (mtm180) REVERT: A 878 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5324 (mtt) REVERT: A 981 TYR cc_start: 0.7099 (t80) cc_final: 0.6546 (t80) REVERT: B 116 LYS cc_start: 0.6802 (tptt) cc_final: 0.6262 (tttt) REVERT: B 781 ASP cc_start: 0.4172 (t0) cc_final: 0.3686 (m-30) REVERT: B 801 MET cc_start: 0.4093 (mtm) cc_final: 0.3712 (ptm) REVERT: B 981 TYR cc_start: 0.6982 (t80) cc_final: 0.6373 (t80) REVERT: C 116 LYS cc_start: 0.6712 (tptt) cc_final: 0.6198 (tttt) REVERT: C 189 MET cc_start: 0.7524 (mtt) cc_final: 0.7114 (mmm) REVERT: C 781 ASP cc_start: 0.4174 (t0) cc_final: 0.3688 (m-30) REVERT: C 801 MET cc_start: 0.4162 (mtm) cc_final: 0.3790 (ptm) REVERT: C 862 ARG cc_start: 0.7274 (mmt180) cc_final: 0.6701 (mtm180) REVERT: D 116 LYS cc_start: 0.6695 (tptt) cc_final: 0.6180 (tttt) REVERT: D 452 ARG cc_start: 0.7234 (tpt90) cc_final: 0.6872 (tmt-80) REVERT: D 781 ASP cc_start: 0.4167 (t0) cc_final: 0.3683 (m-30) REVERT: D 801 MET cc_start: 0.4131 (mtm) cc_final: 0.3748 (ptm) REVERT: D 862 ARG cc_start: 0.7265 (mmt180) cc_final: 0.6690 (mtm180) outliers start: 29 outliers final: 25 residues processed: 304 average time/residue: 0.1645 time to fit residues: 81.7430 Evaluate side-chains 300 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1006 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1006 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 276 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN D 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.214421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178914 restraints weight = 35696.008| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.27 r_work: 0.3988 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26792 Z= 0.170 Angle : 0.600 10.848 36300 Z= 0.316 Chirality : 0.039 0.207 4152 Planarity : 0.004 0.046 4456 Dihedral : 5.566 85.344 3492 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.15 % Allowed : 20.32 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 3104 helix: 2.00 (0.10), residues: 2388 sheet: -2.47 (0.53), residues: 100 loop : -2.21 (0.19), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 842 TYR 0.017 0.001 TYR A 410 PHE 0.030 0.002 PHE A 752 TRP 0.013 0.001 TRP B 994 HIS 0.021 0.002 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (26792) covalent geometry : angle 0.60029 / 0.32 (36300) hydrogen bonds : bond 0.04812 / 3.26 ( 1766) hydrogen bonds : angle 4.12730 / 2.94 ( 5262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.28 seconds wall clock time: 95 minutes 11.13 seconds (5711.13 seconds total)