Starting phenix.real_space_refine on Sat Aug 8 06:53:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjo_65117/08_2026/9vjo_65117.map" } resolution = 2.82 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= 0.012 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 12 5.49 5 S 112 5.16 5 C 16856 2.51 5 N 4220 2.21 5 O 4652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 25854 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6414 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 16, 'TRANS': 781} Chain breaks: 14 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 6414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6414 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 16, 'TRANS': 781} Chain breaks: 14 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 6418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6418 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 14, 'TRANS': 782} Chain breaks: 15 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 6418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6418 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 14, 'TRANS': 782} Chain breaks: 15 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' CA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "B" 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: 4.00, per 1000 atoms: 0.15 Number of scatterers: 25854 At special positions: 0 Unit cell: (149.4, 148.072, 152.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 12 15.00 O 4652 8.00 N 4220 7.00 C 16856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 955.3 milliseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 4 sheets defined 77.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.609A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.661A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 335 through 342 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 386 removed outlier: 3.734A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 468 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 499 Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 519 through 533 removed outlier: 3.599A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.861A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.622A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.757A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.783A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.746A pdb=" N TRP A 651 " --> pdb=" O CYS A 648 " (cutoff:3.500A) 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 728 through 732 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 788 Processing helix chain 'A' and resid 792 through 795 removed outlier: 3.503A pdb=" N THR A 795 " --> pdb=" O ASN A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.809A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 843 removed outlier: 3.592A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 850 removed outlier: 3.614A pdb=" N VAL A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 867 Processing helix chain 'A' and resid 867 through 889 removed outlier: 3.514A pdb=" N LEU A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 988 removed outlier: 3.811A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1008 removed outlier: 4.026A pdb=" N VAL A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1023 removed outlier: 4.123A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1075 through 1104 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.610A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.707A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 335 through 342 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 386 removed outlier: 3.731A pdb=" N GLU C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 454 through 468 removed outlier: 5.201A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.120A 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 499 Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 519 through 533 removed outlier: 3.548A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.862A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.618A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.757A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 645 removed outlier: 3.500A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.750A pdb=" N TRP C 651 " --> pdb=" O CYS C 648 " (cutoff:3.500A) 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 728 through 732 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 788 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 796 through 818 removed outlier: 4.138A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET C 801 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 843 removed outlier: 3.624A pdb=" N ILE C 837 " --> pdb=" O CYS C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 850 removed outlier: 3.607A pdb=" N VAL C 849 " --> pdb=" O ILE C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 867 Processing helix chain 'C' and resid 867 through 889 Processing helix chain 'C' and resid 957 through 988 Processing helix chain 'C' and resid 989 through 1008 removed outlier: 3.915A pdb=" N VAL C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1002 " --> pdb=" O ARG C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1023 removed outlier: 4.120A pdb=" N VAL C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE C1018 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1073 removed outlier: 3.908A pdb=" N THR C1069 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1104 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 158 through 176 removed outlier: 3.576A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.966A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.542A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 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 removed outlier: 3.606A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.908A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 454 through 469 removed outlier: 3.545A pdb=" N LEU D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 530 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.841A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.544A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 removed outlier: 3.528A pdb=" N LEU D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.546A pdb=" N GLU D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 616 " --> pdb=" O GLY D 612 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 621 " --> pdb=" O LEU D 617 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 removed outlier: 3.755A pdb=" N GLU D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.630A pdb=" N TRP D 651 " --> pdb=" O CYS D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.594A pdb=" N ALA D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) 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 723 through 732 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 789 Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'D' and resid 799 through 818 removed outlier: 3.834A pdb=" N LEU D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.581A pdb=" N ILE D 831 " --> pdb=" O SER D 827 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 837 " --> pdb=" O CYS D 833 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 847 removed outlier: 3.705A pdb=" N ILE D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 852 through 890 removed outlier: 4.389A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 869 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.078A pdb=" N THR D 982 " --> pdb=" O MET D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 988 removed outlier: 3.809A pdb=" N VAL D 986 " --> pdb=" O THR D 982 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1008 removed outlier: 3.976A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1073 removed outlier: 3.682A pdb=" N THR D1052 " --> pdb=" O GLU D1048 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D1073 " --> pdb=" O THR D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1104 removed outlier: 3.643A pdb=" N ARG D1079 " --> pdb=" O SER D1075 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D1099 " --> pdb=" O LEU D1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.581A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.968A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.537A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) 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 removed outlier: 3.602A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.915A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.530A pdb=" N LEU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 530 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.841A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.545A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 removed outlier: 3.529A pdb=" N LEU B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.545A pdb=" N GLU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.756A pdb=" N GLU B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.631A pdb=" N TRP B 651 " --> pdb=" O CYS B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.597A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) 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 723 through 732 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 789 Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 799 through 818 removed outlier: 3.837A pdb=" N LEU B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 841 removed outlier: 3.539A pdb=" N ILE B 831 " --> pdb=" O SER B 827 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 837 " --> pdb=" O CYS B 833 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.701A pdb=" N ILE B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 852 through 890 removed outlier: 4.389A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 864 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.089A pdb=" N THR B 982 " --> pdb=" O MET B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 988 removed outlier: 3.831A pdb=" N VAL B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1008 removed outlier: 3.971A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1073 removed outlier: 3.676A pdb=" N THR B1052 " --> pdb=" O GLU B1048 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B1073 " --> pdb=" O THR B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1104 removed outlier: 3.647A pdb=" N ARG B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 263 removed outlier: 6.472A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ALA A 216 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 145 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE A 301 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 259 through 263 removed outlier: 6.469A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ALA C 216 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE C 301 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 117 through 119 removed outlier: 7.130A pdb=" N LEU D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS D 326 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 119 removed outlier: 7.127A pdb=" N LEU B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N CYS B 326 " --> pdb=" O ILE B 301 " (cutoff:3.500A) 1682 hydrogen bonds defined for protein. 4989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 2.53 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: 4102 1.31 - 1.44: 7336 1.44 - 1.56: 14758 1.56 - 1.69: 16 1.69 - 1.81: 176 Bond restraints: 26388 Sorted by residual: bond pdb=" C1A PIO D1201 " pdb=" O2C PIO D1201 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1B PIO C1201 " pdb=" O3C PIO C1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1A PIO B1201 " pdb=" O2C PIO B1201 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1B PIO D1201 " pdb=" O3C PIO D1201 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 26383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 35419 2.40 - 4.79: 280 4.79 - 7.19: 49 7.19 - 9.58: 13 9.58 - 11.98: 9 Bond angle restraints: 35770 Sorted by residual: angle pdb=" CB MET C 161 " pdb=" CG MET C 161 " pdb=" SD MET C 161 " ideal model delta sigma weight residual 112.70 124.68 -11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O1 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O13 PIO D1201 " ideal model delta sigma weight residual 97.64 109.41 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O1 PIO B1201 " pdb=" P1 PIO B1201 " pdb=" O13 PIO B1201 " ideal model delta sigma weight residual 97.64 109.34 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O12 PIO D1201 " ideal model delta sigma weight residual 121.09 109.51 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 PIO B1201 " pdb=" P1 PIO B1201 " pdb=" O12 PIO B1201 " ideal model delta sigma weight residual 121.09 109.55 11.54 3.00e+00 1.11e-01 1.48e+01 ... (remaining 35765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13467 17.92 - 35.84: 1499 35.84 - 53.76: 357 53.76 - 71.69: 111 71.69 - 89.61: 18 Dihedral angle restraints: 15452 sinusoidal: 6052 harmonic: 9400 Sorted by residual: dihedral pdb=" CA HIS A 136 " pdb=" C HIS A 136 " pdb=" N TRP A 137 " pdb=" CA TRP A 137 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA HIS C 136 " pdb=" C HIS C 136 " pdb=" N TRP C 137 " pdb=" CA TRP C 137 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU B 478 " pdb=" C LEU B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 15449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3150 0.032 - 0.064: 648 0.064 - 0.097: 258 0.097 - 0.129: 72 0.129 - 0.161: 10 Chirality restraints: 4138 Sorted by residual: chirality pdb=" CA VAL A 976 " pdb=" N VAL A 976 " pdb=" C VAL A 976 " pdb=" CB VAL A 976 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 983 " pdb=" N VAL A 983 " pdb=" C VAL A 983 " pdb=" CB VAL A 983 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE C 299 " pdb=" N ILE C 299 " pdb=" C ILE C 299 " pdb=" CB ILE C 299 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4135 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 973 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ASN C 973 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN C 973 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 974 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 324 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 325 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 324 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 325 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " 0.025 5.00e-02 4.00e+02 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4987 2.77 - 3.31: 25394 3.31 - 3.84: 40584 3.84 - 4.37: 48232 4.37 - 4.90: 82754 Nonbonded interactions: 201951 Sorted by model distance: nonbonded pdb=" O LEU C 313 " pdb=" OD1 ASN C 317 " model vdw 2.242 3.040 nonbonded pdb=" O LEU A 313 " pdb=" OD1 ASN A 317 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU A 782 " pdb="CA CA A1202 " model vdw 2.314 2.510 nonbonded pdb=" O SER D 319 " pdb=" O SER D 322 " model vdw 2.419 3.040 nonbonded pdb=" O SER B 319 " pdb=" O SER B 322 " model vdw 2.420 3.040 ... (remaining 201946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.069 26388 Z= 0.152 Angle : 0.575 11.976 35770 Z= 0.283 Chirality : 0.034 0.161 4138 Planarity : 0.003 0.044 4376 Dihedral : 16.479 89.607 9308 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 19.37 % Favored : 79.36 % 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: 1.14 (0.15), residues: 3066 helix: 1.43 (0.11), residues: 2218 sheet: -0.61 (0.40), residues: 158 loop : -1.02 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 452 TYR 0.010 0.001 TYR D 117 PHE 0.010 0.001 PHE C 735 TRP 0.018 0.001 TRP A 693 HIS 0.003 0.000 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (26388) covalent geometry : angle 0.57487 / 0.28 (35770) hydrogen bonds : bond 0.22487 / 14.80 ( 1682) hydrogen bonds : angle 6.19564 / 4.47 ( 4989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ILE cc_start: 0.4432 (mm) cc_final: 0.4063 (pt) REVERT: A 533 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5732 (ptp90) REVERT: A 575 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7286 (mp0) REVERT: A 649 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7301 (mp0) REVERT: A 758 MET cc_start: 0.5562 (mmp) cc_final: 0.4315 (ptt) REVERT: A 962 ILE cc_start: 0.7040 (tt) cc_final: 0.6612 (mp) REVERT: A 964 MET cc_start: 0.6488 (ttt) cc_final: 0.5820 (mmt) REVERT: A 991 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (t0) REVERT: C 126 SER cc_start: 0.8086 (p) cc_final: 0.7766 (m) REVERT: C 161 MET cc_start: 0.5112 (mpp) cc_final: 0.4911 (mmt) REVERT: C 288 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7312 (tmt-80) REVERT: C 378 ILE cc_start: 0.4390 (mm) cc_final: 0.3786 (pt) REVERT: C 381 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6446 (tt) REVERT: C 533 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6068 (ptp90) REVERT: C 575 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7296 (mp0) REVERT: C 649 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7369 (mp0) REVERT: C 758 MET cc_start: 0.4942 (mmp) cc_final: 0.3996 (ptt) REVERT: C 964 MET cc_start: 0.6556 (ttt) cc_final: 0.5861 (mmt) REVERT: D 140 LYS cc_start: 0.8111 (tppt) cc_final: 0.7578 (ttpt) REVERT: D 162 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5829 (mtm-85) REVERT: D 288 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6849 (mmm160) REVERT: D 295 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: D 313 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6628 (mm) REVERT: D 318 THR cc_start: 0.7586 (p) cc_final: 0.7313 (t) REVERT: D 353 MET cc_start: 0.5906 (mpp) cc_final: 0.5514 (mpp) REVERT: D 396 MET cc_start: 0.5196 (tpt) cc_final: 0.4879 (mmm) REVERT: D 435 GLU cc_start: 0.8039 (tp30) cc_final: 0.7443 (tp30) REVERT: D 574 LYS cc_start: 0.8635 (mtpm) cc_final: 0.7640 (mptt) REVERT: D 575 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7405 (mp0) REVERT: D 662 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7434 (mt-10) REVERT: D 697 LEU cc_start: 0.7076 (tm) cc_final: 0.6294 (mt) REVERT: D 701 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.6005 (pp) REVERT: D 1051 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7486 (mp0) REVERT: D 1066 LYS cc_start: 0.7077 (ttmm) cc_final: 0.6740 (mtpt) REVERT: B 140 LYS cc_start: 0.8081 (tppt) cc_final: 0.7562 (ttpt) REVERT: B 162 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5823 (mtm-85) REVERT: B 288 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6792 (mmm160) REVERT: B 295 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: B 313 LEU cc_start: 0.6877 (mm) cc_final: 0.6598 (mm) REVERT: B 318 THR cc_start: 0.7594 (p) cc_final: 0.7333 (t) REVERT: B 353 MET cc_start: 0.5861 (mpp) cc_final: 0.5527 (mpp) REVERT: B 396 MET cc_start: 0.5187 (tpt) cc_final: 0.4873 (mmm) REVERT: B 435 GLU cc_start: 0.8039 (tp30) cc_final: 0.7446 (tp30) REVERT: B 460 GLU cc_start: 0.7324 (tp30) cc_final: 0.7047 (mp0) REVERT: B 485 GLN cc_start: 0.7125 (tt0) cc_final: 0.6779 (mt0) REVERT: B 574 LYS cc_start: 0.8623 (mtpm) cc_final: 0.7621 (mptt) REVERT: B 575 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7403 (mp0) REVERT: B 662 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7435 (mt-10) REVERT: B 697 LEU cc_start: 0.7066 (tm) cc_final: 0.6284 (mt) REVERT: B 701 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.5990 (pp) REVERT: B 1051 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7552 (mp0) outliers start: 35 outliers final: 17 residues processed: 334 average time/residue: 0.5301 time to fit residues: 208.7493 Evaluate side-chains 321 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 991 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS D 294 ASN D 459 GLN D 483 ASN D 987 GLN D 989 ASN B 459 GLN B 483 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122872 restraints weight = 30901.508| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.10 r_work: 0.3266 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26388 Z= 0.265 Angle : 0.649 8.259 35770 Z= 0.340 Chirality : 0.044 0.207 4138 Planarity : 0.005 0.059 4376 Dihedral : 7.286 83.246 3512 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.27 % Allowed : 16.70 % Favored : 79.03 % 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: 3066 helix: 1.46 (0.11), residues: 2298 sheet: -0.67 (0.41), residues: 160 loop : -1.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 452 TYR 0.018 0.002 TYR D 284 PHE 0.023 0.002 PHE A 979 TRP 0.019 0.002 TRP C 453 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.26 (26388) covalent geometry : angle 0.64934 / 0.34 (35770) hydrogen bonds : bond 0.08011 / 5.32 ( 1682) hydrogen bonds : angle 4.28194 / 3.09 ( 4989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 335 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6338 (mtm) REVERT: A 283 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7322 (tptt) REVERT: A 381 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6286 (tt) REVERT: A 575 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7650 (mp0) REVERT: A 758 MET cc_start: 0.5683 (mmp) cc_final: 0.4357 (ptt) REVERT: A 822 LYS cc_start: 0.7177 (mppt) cc_final: 0.6833 (mmtt) REVERT: A 964 MET cc_start: 0.6855 (ttt) cc_final: 0.6109 (mmt) REVERT: A 1011 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7048 (mt) REVERT: C 283 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7301 (tptt) REVERT: C 445 GLU cc_start: 0.7568 (mp0) cc_final: 0.7350 (mp0) REVERT: C 533 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.5813 (ptp90) REVERT: C 575 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7654 (mp0) REVERT: C 758 MET cc_start: 0.5526 (mmp) cc_final: 0.4311 (ptt) REVERT: C 964 MET cc_start: 0.6905 (ttt) cc_final: 0.6150 (mmt) REVERT: C 1011 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7045 (mt) REVERT: D 140 LYS cc_start: 0.8250 (tppt) cc_final: 0.7599 (ttpt) REVERT: D 260 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (mp) REVERT: D 295 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: D 353 MET cc_start: 0.6197 (mpp) cc_final: 0.5976 (mpp) REVERT: D 435 GLU cc_start: 0.8126 (tp30) cc_final: 0.7678 (tp30) REVERT: D 521 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8287 (tm) REVERT: D 662 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7573 (mt-10) REVERT: D 697 LEU cc_start: 0.6850 (tm) cc_final: 0.6178 (mt) REVERT: D 851 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6772 (ttt-90) REVERT: D 1051 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7297 (mp0) REVERT: D 1066 LYS cc_start: 0.6876 (ttmm) cc_final: 0.6434 (tptt) REVERT: B 140 LYS cc_start: 0.8225 (tppt) cc_final: 0.7575 (ttpt) REVERT: B 283 LYS cc_start: 0.6995 (mmmt) cc_final: 0.6702 (mmtt) REVERT: B 295 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: B 313 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6581 (mm) REVERT: B 353 MET cc_start: 0.6251 (mpp) cc_final: 0.6043 (mpp) REVERT: B 435 GLU cc_start: 0.8145 (tp30) cc_final: 0.7709 (tp30) REVERT: B 445 GLU cc_start: 0.7241 (mp0) cc_final: 0.6997 (mp0) REVERT: B 460 GLU cc_start: 0.7056 (tp30) cc_final: 0.6827 (mp0) REVERT: B 485 GLN cc_start: 0.7547 (tt0) cc_final: 0.7193 (mt0) REVERT: B 521 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8273 (tm) REVERT: B 662 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7591 (mt-10) REVERT: B 697 LEU cc_start: 0.6830 (tm) cc_final: 0.6169 (mt) REVERT: B 851 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6774 (ttt-90) REVERT: B 1051 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7358 (mp0) outliers start: 117 outliers final: 51 residues processed: 413 average time/residue: 0.4971 time to fit residues: 242.6694 Evaluate side-chains 362 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 255 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 295 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 247 optimal weight: 0.3980 chunk 204 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 799 ASN B 294 ASN B 799 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.193250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130024 restraints weight = 30893.764| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.30 r_work: 0.3332 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26388 Z= 0.118 Angle : 0.466 6.422 35770 Z= 0.250 Chirality : 0.037 0.150 4138 Planarity : 0.004 0.054 4376 Dihedral : 6.209 83.663 3464 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.61 % Allowed : 18.49 % Favored : 77.90 % 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: 3066 helix: 2.04 (0.11), residues: 2310 sheet: -0.50 (0.40), residues: 160 loop : -1.35 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 452 TYR 0.018 0.001 TYR B 284 PHE 0.023 0.001 PHE C 979 TRP 0.021 0.001 TRP A 693 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (26388) covalent geometry : angle 0.46568 / 0.25 (35770) hydrogen bonds : bond 0.04998 / 3.31 ( 1682) hydrogen bonds : angle 3.77124 / 2.72 ( 4989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 311 time to evaluate : 0.949 Fit side-chains REVERT: A 283 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7245 (tptt) REVERT: A 378 ILE cc_start: 0.4536 (mm) cc_final: 0.3721 (pt) REVERT: A 381 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6205 (tt) REVERT: A 533 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.5707 (ptp90) REVERT: A 575 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7590 (mp0) REVERT: A 631 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: A 649 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7753 (mp0) REVERT: A 758 MET cc_start: 0.5246 (mmp) cc_final: 0.4019 (ptt) REVERT: A 822 LYS cc_start: 0.6943 (mppt) cc_final: 0.6606 (mmtt) REVERT: A 964 MET cc_start: 0.6646 (ttt) cc_final: 0.5969 (mmt) REVERT: C 283 LYS cc_start: 0.7634 (mmtp) cc_final: 0.7279 (tptt) REVERT: C 378 ILE cc_start: 0.4477 (mm) cc_final: 0.3716 (pt) REVERT: C 381 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6141 (tt) REVERT: C 445 GLU cc_start: 0.7500 (mp0) cc_final: 0.7258 (mp0) REVERT: C 575 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7594 (mp0) REVERT: C 631 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: C 649 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7731 (mp0) REVERT: C 758 MET cc_start: 0.5147 (mmp) cc_final: 0.3993 (ptt) REVERT: C 964 MET cc_start: 0.6679 (ttt) cc_final: 0.5998 (mmt) REVERT: C 971 LEU cc_start: 0.7720 (tp) cc_final: 0.7386 (mp) REVERT: D 140 LYS cc_start: 0.8252 (tppt) cc_final: 0.7574 (ttpt) REVERT: D 295 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: D 313 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6682 (mm) REVERT: D 353 MET cc_start: 0.6337 (mpp) cc_final: 0.6125 (mpp) REVERT: D 395 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.4710 (mppt) REVERT: D 435 GLU cc_start: 0.7998 (tp30) cc_final: 0.7653 (tp30) REVERT: D 662 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7525 (mt-10) REVERT: D 667 HIS cc_start: 0.8282 (m-70) cc_final: 0.7683 (t70) REVERT: D 697 LEU cc_start: 0.6802 (tm) cc_final: 0.6156 (mt) REVERT: D 1051 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7029 (mp0) REVERT: D 1066 LYS cc_start: 0.6646 (ttmm) cc_final: 0.6210 (tptt) REVERT: B 140 LYS cc_start: 0.8240 (tppt) cc_final: 0.7563 (ttpt) REVERT: B 295 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: B 313 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6597 (mm) REVERT: B 353 MET cc_start: 0.6325 (mpp) cc_final: 0.6118 (mpp) REVERT: B 395 LYS cc_start: 0.5903 (OUTLIER) cc_final: 0.4672 (mppt) REVERT: B 435 GLU cc_start: 0.8029 (tp30) cc_final: 0.7674 (tp30) REVERT: B 445 GLU cc_start: 0.7304 (mp0) cc_final: 0.7013 (mp0) REVERT: B 662 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7547 (mt-10) REVERT: B 667 HIS cc_start: 0.8260 (m-70) cc_final: 0.7659 (t70) REVERT: B 697 LEU cc_start: 0.6794 (tm) cc_final: 0.6164 (mt) REVERT: B 1051 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7068 (mp0) outliers start: 99 outliers final: 46 residues processed: 374 average time/residue: 0.4854 time to fit residues: 214.9416 Evaluate side-chains 336 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 761 HIS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 761 HIS Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 249 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 317 ASN ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 317 ASN ** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.191635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128403 restraints weight = 30470.397| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.03 r_work: 0.3320 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26388 Z= 0.155 Angle : 0.521 7.506 35770 Z= 0.272 Chirality : 0.039 0.154 4138 Planarity : 0.004 0.089 4376 Dihedral : 6.034 84.757 3458 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.56 % Allowed : 18.09 % Favored : 77.35 % 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: 1.92 (0.15), residues: 3066 helix: 2.05 (0.11), residues: 2314 sheet: -0.37 (0.41), residues: 158 loop : -1.46 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 119 TYR 0.019 0.001 TYR D 284 PHE 0.023 0.001 PHE A 979 TRP 0.022 0.002 TRP A 693 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (26388) covalent geometry : angle 0.52082 / 0.27 (35770) hydrogen bonds : bond 0.05755 / 3.82 ( 1682) hydrogen bonds : angle 3.72343 / 2.69 ( 4989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 308 time to evaluate : 0.916 Fit side-chains REVERT: A 283 LYS cc_start: 0.7670 (mmtp) cc_final: 0.7268 (tptt) REVERT: A 381 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6269 (tt) REVERT: A 482 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 533 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5926 (ptp90) REVERT: A 575 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7575 (mp0) REVERT: A 605 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7046 (mttp) REVERT: A 631 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 758 MET cc_start: 0.5314 (mmp) cc_final: 0.4093 (ptt) REVERT: A 822 LYS cc_start: 0.7028 (mppt) cc_final: 0.6708 (mmtt) REVERT: A 964 MET cc_start: 0.6674 (ttt) cc_final: 0.5977 (mmt) REVERT: C 189 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6472 (mtm) REVERT: C 283 LYS cc_start: 0.7674 (mmtp) cc_final: 0.7312 (tptt) REVERT: C 378 ILE cc_start: 0.4495 (mm) cc_final: 0.3692 (pt) REVERT: C 381 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6238 (tt) REVERT: C 575 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7575 (mp0) REVERT: C 605 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7064 (mttp) REVERT: C 631 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: C 758 MET cc_start: 0.5323 (mmp) cc_final: 0.4109 (ptt) REVERT: C 964 MET cc_start: 0.6702 (ttt) cc_final: 0.6019 (mmt) REVERT: D 140 LYS cc_start: 0.8252 (tppt) cc_final: 0.7578 (ttpt) REVERT: D 295 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: D 313 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6717 (mm) REVERT: D 353 MET cc_start: 0.6359 (mpp) cc_final: 0.6092 (mpp) REVERT: D 395 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.4734 (mppt) REVERT: D 435 GLU cc_start: 0.7981 (tp30) cc_final: 0.7586 (tp30) REVERT: D 521 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8192 (tm) REVERT: D 574 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7316 (mptt) REVERT: D 662 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7566 (mt-10) REVERT: D 667 HIS cc_start: 0.8259 (m-70) cc_final: 0.7687 (t70) REVERT: D 697 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6161 (mt) REVERT: D 1051 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7094 (mp0) REVERT: D 1066 LYS cc_start: 0.6682 (ttmm) cc_final: 0.6203 (tptt) REVERT: B 140 LYS cc_start: 0.8228 (tppt) cc_final: 0.7553 (ttpt) REVERT: B 295 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: B 313 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6617 (mm) REVERT: B 353 MET cc_start: 0.6399 (mpp) cc_final: 0.6134 (mpp) REVERT: B 395 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.4719 (mppt) REVERT: B 435 GLU cc_start: 0.8013 (tp30) cc_final: 0.7642 (tp30) REVERT: B 445 GLU cc_start: 0.7310 (mp0) cc_final: 0.7010 (mp0) REVERT: B 521 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (tm) REVERT: B 574 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: B 662 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7583 (mt-10) REVERT: B 667 HIS cc_start: 0.8248 (m-70) cc_final: 0.7668 (t70) REVERT: B 697 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6143 (mt) REVERT: B 1051 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7137 (mp0) outliers start: 125 outliers final: 62 residues processed: 392 average time/residue: 0.5281 time to fit residues: 245.4276 Evaluate side-chains 378 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 295 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1015 PHE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 202 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN B 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.191702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128528 restraints weight = 30588.543| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.03 r_work: 0.3317 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26388 Z= 0.154 Angle : 0.515 7.792 35770 Z= 0.269 Chirality : 0.039 0.151 4138 Planarity : 0.004 0.079 4376 Dihedral : 5.942 84.154 3454 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.63 % Allowed : 18.56 % Favored : 76.81 % 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: 1.93 (0.15), residues: 3066 helix: 2.06 (0.11), residues: 2314 sheet: -0.33 (0.41), residues: 158 loop : -1.49 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 119 TYR 0.025 0.001 TYR B 284 PHE 0.018 0.001 PHE A 979 TRP 0.024 0.002 TRP A 693 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (26388) covalent geometry : angle 0.51471 / 0.27 (35770) hydrogen bonds : bond 0.05561 / 3.69 ( 1682) hydrogen bonds : angle 3.70067 / 2.67 ( 4989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 303 time to evaluate : 1.131 Fit side-chains REVERT: A 189 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: A 283 LYS cc_start: 0.7656 (mmtp) cc_final: 0.7276 (tptt) REVERT: A 381 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6273 (tt) REVERT: A 533 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.5918 (ptp90) REVERT: A 575 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7594 (mp0) REVERT: A 605 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7057 (mttp) REVERT: A 631 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: A 758 MET cc_start: 0.5390 (mmp) cc_final: 0.4102 (ptt) REVERT: A 964 MET cc_start: 0.6691 (ttt) cc_final: 0.5994 (mmt) REVERT: C 126 SER cc_start: 0.8060 (p) cc_final: 0.7691 (m) REVERT: C 283 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7307 (tptt) REVERT: C 378 ILE cc_start: 0.4452 (mm) cc_final: 0.3759 (pt) REVERT: C 381 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6192 (tt) REVERT: C 445 GLU cc_start: 0.7530 (mp0) cc_final: 0.7281 (mp0) REVERT: C 575 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7586 (mp0) REVERT: C 605 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7071 (mttp) REVERT: C 631 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: C 758 MET cc_start: 0.5393 (mmp) cc_final: 0.4135 (ptt) REVERT: C 964 MET cc_start: 0.6706 (ttt) cc_final: 0.6015 (mmt) REVERT: D 140 LYS cc_start: 0.8268 (tppt) cc_final: 0.7567 (ttpt) REVERT: D 295 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: D 313 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6675 (mm) REVERT: D 353 MET cc_start: 0.6386 (mpp) cc_final: 0.6071 (mpp) REVERT: D 395 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.4780 (mppt) REVERT: D 435 GLU cc_start: 0.8026 (tp30) cc_final: 0.7632 (tp30) REVERT: D 452 ARG cc_start: 0.2467 (OUTLIER) cc_final: 0.2263 (tpm170) REVERT: D 574 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7307 (mptt) REVERT: D 662 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7561 (mt-10) REVERT: D 667 HIS cc_start: 0.8246 (m-70) cc_final: 0.7675 (t70) REVERT: D 697 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6178 (mt) REVERT: D 1051 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7095 (mp0) REVERT: D 1066 LYS cc_start: 0.6738 (ttmm) cc_final: 0.6235 (tptt) REVERT: B 140 LYS cc_start: 0.8244 (tppt) cc_final: 0.7554 (ttpt) REVERT: B 295 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: B 353 MET cc_start: 0.6459 (mpp) cc_final: 0.6216 (mpp) REVERT: B 395 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.4679 (mppt) REVERT: B 435 GLU cc_start: 0.8025 (tp30) cc_final: 0.7708 (tp30) REVERT: B 662 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7583 (mt-10) REVERT: B 667 HIS cc_start: 0.8235 (m-70) cc_final: 0.7657 (t70) REVERT: B 697 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6162 (mt) REVERT: B 1051 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7146 (mp0) outliers start: 127 outliers final: 64 residues processed: 391 average time/residue: 0.5874 time to fit residues: 270.7100 Evaluate side-chains 363 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 282 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 292 optimal weight: 10.0000 chunk 285 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 235 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 480 ASN D 765 HIS D 987 GLN B 222 ASN B 294 ASN B 765 HIS B 987 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123782 restraints weight = 30688.912| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.04 r_work: 0.3257 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 26388 Z= 0.287 Angle : 0.670 8.549 35770 Z= 0.345 Chirality : 0.046 0.230 4138 Planarity : 0.005 0.098 4376 Dihedral : 6.479 83.176 3454 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.65 % Allowed : 18.20 % Favored : 76.15 % 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: 1.24 (0.15), residues: 3066 helix: 1.55 (0.11), residues: 2312 sheet: -0.44 (0.42), residues: 160 loop : -1.70 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 452 TYR 0.021 0.002 TYR C 117 PHE 0.024 0.002 PHE A 165 TRP 0.025 0.003 TRP A 693 HIS 0.005 0.001 HIS C 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.29 (26388) covalent geometry : angle 0.67008 / 0.34 (35770) hydrogen bonds : bond 0.07745 / 5.15 ( 1682) hydrogen bonds : angle 4.02985 / 2.90 ( 4989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 309 time to evaluate : 1.016 Fit side-chains REVERT: A 189 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6295 (mtm) REVERT: A 197 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6531 (ttm170) REVERT: A 283 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7355 (tptt) REVERT: A 533 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6037 (ptp90) REVERT: A 575 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7706 (mp0) REVERT: A 605 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7169 (mttp) REVERT: A 631 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: A 685 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 758 MET cc_start: 0.5865 (mmp) cc_final: 0.4447 (ptt) REVERT: A 964 MET cc_start: 0.6996 (ttt) cc_final: 0.6219 (mmt) REVERT: A 1011 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7367 (mt) REVERT: C 189 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6575 (mtm) REVERT: C 283 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7360 (tptt) REVERT: C 575 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7698 (mp0) REVERT: C 605 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7175 (mttp) REVERT: C 631 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: C 685 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 758 MET cc_start: 0.5848 (mmp) cc_final: 0.4492 (ptt) REVERT: C 964 MET cc_start: 0.7003 (ttt) cc_final: 0.6234 (mmt) REVERT: C 1011 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7372 (mt) REVERT: D 140 LYS cc_start: 0.8310 (tppt) cc_final: 0.7596 (ttpt) REVERT: D 295 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: D 313 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6687 (mm) REVERT: D 353 MET cc_start: 0.6501 (mpp) cc_final: 0.6189 (mpp) REVERT: D 395 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.4990 (mppt) REVERT: D 435 GLU cc_start: 0.8195 (tp30) cc_final: 0.7737 (tp30) REVERT: D 452 ARG cc_start: 0.2518 (OUTLIER) cc_final: 0.1943 (tpm170) REVERT: D 574 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7451 (mptt) REVERT: D 638 ASP cc_start: 0.8051 (t0) cc_final: 0.7455 (m-30) REVERT: D 662 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7613 (mt-10) REVERT: D 667 HIS cc_start: 0.8274 (m-70) cc_final: 0.7737 (t70) REVERT: D 697 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6213 (mt) REVERT: D 698 CYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7235 (t) REVERT: D 851 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6786 (ttt-90) REVERT: D 1051 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7388 (mp0) REVERT: B 140 LYS cc_start: 0.8296 (tppt) cc_final: 0.7577 (ttpt) REVERT: B 295 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: B 313 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6857 (mm) REVERT: B 353 MET cc_start: 0.6520 (mpp) cc_final: 0.6215 (mpp) REVERT: B 395 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.4902 (mppt) REVERT: B 435 GLU cc_start: 0.8218 (tp30) cc_final: 0.7760 (tp30) REVERT: B 452 ARG cc_start: 0.2670 (OUTLIER) cc_final: 0.1904 (tpm170) REVERT: B 574 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7457 (mptt) REVERT: B 638 ASP cc_start: 0.8069 (t0) cc_final: 0.7476 (m-30) REVERT: B 662 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7626 (mt-10) REVERT: B 667 HIS cc_start: 0.8271 (m-70) cc_final: 0.7724 (t70) REVERT: B 697 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6208 (mt) REVERT: B 698 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7206 (t) REVERT: B 1051 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7429 (mp0) outliers start: 155 outliers final: 83 residues processed: 419 average time/residue: 0.5725 time to fit residues: 283.5136 Evaluate side-chains 402 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 294 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1015 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1004 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1004 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 251 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 158 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 294 ASN D 765 HIS ** D 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 294 ASN B 765 HIS ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.191420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127944 restraints weight = 30689.609| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.05 r_work: 0.3313 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26388 Z= 0.141 Angle : 0.519 8.120 35770 Z= 0.272 Chirality : 0.038 0.150 4138 Planarity : 0.004 0.086 4376 Dihedral : 6.152 84.825 3454 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.27 % Allowed : 20.13 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.15), residues: 3066 helix: 1.95 (0.11), residues: 2318 sheet: -0.39 (0.41), residues: 158 loop : -1.68 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 452 TYR 0.025 0.001 TYR D 284 PHE 0.019 0.001 PHE A 979 TRP 0.030 0.002 TRP A 693 HIS 0.002 0.001 HIS C 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (26388) covalent geometry : angle 0.51895 / 0.27 (35770) hydrogen bonds : bond 0.05291 / 3.50 ( 1682) hydrogen bonds : angle 3.72242 / 2.68 ( 4989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 296 time to evaluate : 0.926 Fit side-chains REVERT: A 189 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6264 (mtm) REVERT: A 283 LYS cc_start: 0.7713 (mmtp) cc_final: 0.7321 (tptt) REVERT: A 533 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5970 (ptp90) REVERT: A 575 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7623 (mp0) REVERT: A 631 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: A 685 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 758 MET cc_start: 0.5640 (mmp) cc_final: 0.4275 (ptt) REVERT: A 964 MET cc_start: 0.6790 (ttt) cc_final: 0.6071 (mmt) REVERT: C 189 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6374 (mtm) REVERT: C 283 LYS cc_start: 0.7677 (mmtp) cc_final: 0.7442 (mmtm) REVERT: C 378 ILE cc_start: 0.4479 (mm) cc_final: 0.3784 (pt) REVERT: C 445 GLU cc_start: 0.7611 (mp0) cc_final: 0.7390 (mp0) REVERT: C 533 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5806 (ptp90) REVERT: C 575 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7605 (mp0) REVERT: C 631 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: C 685 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 758 MET cc_start: 0.5646 (mmp) cc_final: 0.4284 (ptt) REVERT: C 964 MET cc_start: 0.6821 (ttt) cc_final: 0.6088 (mmt) REVERT: C 979 PHE cc_start: 0.7292 (t80) cc_final: 0.7008 (t80) REVERT: D 140 LYS cc_start: 0.8291 (tppt) cc_final: 0.7568 (ttpt) REVERT: D 295 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: D 353 MET cc_start: 0.6481 (mpp) cc_final: 0.6152 (mpp) REVERT: D 395 LYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5166 (mtpp) REVERT: D 435 GLU cc_start: 0.8135 (tp30) cc_final: 0.7754 (tp30) REVERT: D 452 ARG cc_start: 0.2531 (OUTLIER) cc_final: 0.1934 (tpm170) REVERT: D 574 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7312 (mptt) REVERT: D 662 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7603 (mt-10) REVERT: D 667 HIS cc_start: 0.8280 (m-70) cc_final: 0.7704 (t70) REVERT: D 697 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6176 (mt) REVERT: D 698 CYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7061 (t) REVERT: D 1051 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7124 (mp0) REVERT: B 127 GLU cc_start: 0.7725 (tp30) cc_final: 0.7381 (mt-10) REVERT: B 140 LYS cc_start: 0.8285 (tppt) cc_final: 0.7544 (ttpt) REVERT: B 295 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: B 313 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6884 (mm) REVERT: B 353 MET cc_start: 0.6499 (mpp) cc_final: 0.6199 (mpp) REVERT: B 395 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.4860 (mppt) REVERT: B 435 GLU cc_start: 0.8147 (tp30) cc_final: 0.7776 (tp30) REVERT: B 574 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7298 (mptt) REVERT: B 662 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7627 (mt-10) REVERT: B 667 HIS cc_start: 0.8273 (m-70) cc_final: 0.7697 (t70) REVERT: B 697 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6159 (mt) REVERT: B 698 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7049 (t) REVERT: B 851 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6767 (ttt-90) REVERT: B 987 GLN cc_start: 0.7876 (mm110) cc_final: 0.7597 (mp10) REVERT: B 1051 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7172 (mp0) outliers start: 117 outliers final: 60 residues processed: 374 average time/residue: 0.5145 time to fit residues: 228.0367 Evaluate side-chains 365 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 761 HIS Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 211 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 334 GLN D 987 GLN B 222 ASN B 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127016 restraints weight = 30780.786| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.07 r_work: 0.3311 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26388 Z= 0.146 Angle : 0.530 8.516 35770 Z= 0.274 Chirality : 0.039 0.157 4138 Planarity : 0.004 0.082 4376 Dihedral : 6.079 85.042 3454 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.94 % Allowed : 20.64 % Favored : 75.42 % 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: 3066 helix: 2.03 (0.11), residues: 2316 sheet: -0.34 (0.40), residues: 158 loop : -1.63 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.024 0.001 TYR D 284 PHE 0.014 0.001 PHE C 735 TRP 0.037 0.002 TRP A 693 HIS 0.002 0.001 HIS C 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (26388) covalent geometry : angle 0.53016 / 0.27 (35770) hydrogen bonds : bond 0.05368 / 3.56 ( 1682) hydrogen bonds : angle 3.67350 / 2.65 ( 4989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 296 time to evaluate : 0.850 Fit side-chains REVERT: A 189 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6284 (mtm) REVERT: A 280 GLN cc_start: 0.7862 (tt0) cc_final: 0.7625 (tm-30) REVERT: A 283 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7324 (tptt) REVERT: A 533 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5952 (ptp90) REVERT: A 575 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7595 (mp0) REVERT: A 605 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7078 (mttp) REVERT: A 631 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: A 685 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 758 MET cc_start: 0.5452 (mmp) cc_final: 0.4167 (ptt) REVERT: A 964 MET cc_start: 0.6731 (ttt) cc_final: 0.6021 (mmt) REVERT: C 126 SER cc_start: 0.8095 (p) cc_final: 0.7712 (m) REVERT: C 189 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6402 (mtm) REVERT: C 283 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7458 (mmtm) REVERT: C 378 ILE cc_start: 0.4448 (mm) cc_final: 0.3754 (pt) REVERT: C 445 GLU cc_start: 0.7599 (mp0) cc_final: 0.7344 (mp0) REVERT: C 533 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5774 (ptp90) REVERT: C 575 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7582 (mp0) REVERT: C 605 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7092 (mttp) REVERT: C 631 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: C 685 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 758 MET cc_start: 0.5506 (mmp) cc_final: 0.4190 (ptt) REVERT: C 964 MET cc_start: 0.6773 (ttt) cc_final: 0.6066 (mmt) REVERT: D 140 LYS cc_start: 0.8263 (tppt) cc_final: 0.7532 (ttpt) REVERT: D 295 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: D 353 MET cc_start: 0.6496 (mpp) cc_final: 0.6166 (mpp) REVERT: D 395 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5231 (mtpp) REVERT: D 435 GLU cc_start: 0.8127 (tp30) cc_final: 0.7735 (tp30) REVERT: D 452 ARG cc_start: 0.2405 (OUTLIER) cc_final: 0.1814 (tpm170) REVERT: D 574 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7286 (mptt) REVERT: D 638 ASP cc_start: 0.7908 (t0) cc_final: 0.7273 (m-30) REVERT: D 662 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7601 (mt-10) REVERT: D 667 HIS cc_start: 0.8276 (m-70) cc_final: 0.7696 (t70) REVERT: D 697 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6158 (mt) REVERT: D 1051 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7101 (mp0) REVERT: D 1066 LYS cc_start: 0.6779 (ttmm) cc_final: 0.6270 (tptt) REVERT: B 127 GLU cc_start: 0.7721 (tp30) cc_final: 0.7361 (mt-10) REVERT: B 140 LYS cc_start: 0.8262 (tppt) cc_final: 0.7515 (ttpt) REVERT: B 295 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: B 313 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6819 (mm) REVERT: B 353 MET cc_start: 0.6518 (mpp) cc_final: 0.6202 (mpp) REVERT: B 395 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5131 (mtpp) REVERT: B 435 GLU cc_start: 0.8139 (tp30) cc_final: 0.7756 (tp30) REVERT: B 574 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7287 (mptt) REVERT: B 638 ASP cc_start: 0.7936 (t0) cc_final: 0.7303 (m-30) REVERT: B 662 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7621 (mt-10) REVERT: B 667 HIS cc_start: 0.8254 (m-70) cc_final: 0.7665 (t70) REVERT: B 697 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6143 (mt) REVERT: B 987 GLN cc_start: 0.7802 (mm110) cc_final: 0.7477 (mp10) REVERT: B 1051 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7131 (mp0) outliers start: 108 outliers final: 72 residues processed: 378 average time/residue: 0.5161 time to fit residues: 230.7633 Evaluate side-chains 371 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 281 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 991 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 278 optimal weight: 0.0980 chunk 264 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 151 optimal weight: 0.0270 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 overall best weight: 1.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.193077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135879 restraints weight = 30712.208| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.19 r_work: 0.3339 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26388 Z= 0.120 Angle : 0.494 8.823 35770 Z= 0.257 Chirality : 0.037 0.147 4138 Planarity : 0.004 0.078 4376 Dihedral : 5.888 85.422 3454 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.50 % Allowed : 21.59 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.15), residues: 3066 helix: 2.19 (0.11), residues: 2316 sheet: -0.26 (0.40), residues: 158 loop : -1.54 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.020 0.001 TYR B 284 PHE 0.024 0.001 PHE A 979 TRP 0.042 0.002 TRP A 693 HIS 0.002 0.000 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (26388) covalent geometry : angle 0.49357 / 0.26 (35770) hydrogen bonds : bond 0.04580 / 3.03 ( 1682) hydrogen bonds : angle 3.57794 / 2.58 ( 4989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 294 time to evaluate : 1.229 Fit side-chains REVERT: A 280 GLN cc_start: 0.7866 (tt0) cc_final: 0.7643 (tm-30) REVERT: A 283 LYS cc_start: 0.7693 (mmtp) cc_final: 0.7455 (mmtm) REVERT: A 355 LYS cc_start: 0.7315 (tppp) cc_final: 0.7026 (mmmm) REVERT: A 533 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5947 (ptp90) REVERT: A 575 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7643 (mp0) REVERT: A 605 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7074 (mttp) REVERT: A 631 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: A 685 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 758 MET cc_start: 0.5367 (mmp) cc_final: 0.4102 (ptt) REVERT: A 964 MET cc_start: 0.6663 (ttt) cc_final: 0.5986 (mmt) REVERT: C 126 SER cc_start: 0.8065 (p) cc_final: 0.7725 (m) REVERT: C 189 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6404 (mtm) REVERT: C 283 LYS cc_start: 0.7742 (mmtp) cc_final: 0.7516 (mmtm) REVERT: C 378 ILE cc_start: 0.4473 (mm) cc_final: 0.3814 (pt) REVERT: C 533 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5797 (ptp90) REVERT: C 575 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7620 (mp0) REVERT: C 605 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7081 (mttp) REVERT: C 631 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: C 649 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7795 (mp0) REVERT: C 685 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8097 (mm-30) REVERT: C 758 MET cc_start: 0.5413 (mmp) cc_final: 0.4155 (ptt) REVERT: C 964 MET cc_start: 0.6692 (ttt) cc_final: 0.6015 (mmt) REVERT: C 971 LEU cc_start: 0.7802 (tp) cc_final: 0.7570 (mp) REVERT: C 979 PHE cc_start: 0.7326 (t80) cc_final: 0.7072 (t80) REVERT: D 106 ILE cc_start: 0.6778 (mt) cc_final: 0.6498 (tt) REVERT: D 127 GLU cc_start: 0.7676 (tp30) cc_final: 0.7330 (mt-10) REVERT: D 140 LYS cc_start: 0.8242 (tppt) cc_final: 0.7479 (ttpt) REVERT: D 295 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: D 353 MET cc_start: 0.6517 (mpp) cc_final: 0.6198 (mpp) REVERT: D 395 LYS cc_start: 0.6126 (OUTLIER) cc_final: 0.5251 (mtpp) REVERT: D 435 GLU cc_start: 0.8113 (tp30) cc_final: 0.7727 (tp30) REVERT: D 452 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1791 (tpm170) REVERT: D 662 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7616 (mt-10) REVERT: D 697 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6188 (mt) REVERT: D 1051 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7111 (mp0) REVERT: D 1066 LYS cc_start: 0.6744 (ttmm) cc_final: 0.6245 (tptt) REVERT: B 140 LYS cc_start: 0.8246 (tppt) cc_final: 0.7480 (ttpt) REVERT: B 295 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: B 353 MET cc_start: 0.6560 (mpp) cc_final: 0.6247 (mpp) REVERT: B 395 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5181 (mtpp) REVERT: B 435 GLU cc_start: 0.8085 (tp30) cc_final: 0.7723 (tp30) REVERT: B 574 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7301 (mptt) REVERT: B 662 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7641 (mt-10) REVERT: B 697 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6166 (mt) REVERT: B 698 CYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7046 (t) REVERT: B 890 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5357 (ptm-80) REVERT: B 987 GLN cc_start: 0.7846 (mm110) cc_final: 0.7541 (mp10) REVERT: B 1051 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7143 (mp0) REVERT: B 1066 LYS cc_start: 0.6815 (mtpt) cc_final: 0.6188 (tptt) outliers start: 96 outliers final: 59 residues processed: 364 average time/residue: 0.5610 time to fit residues: 242.4261 Evaluate side-chains 357 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 991 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 180 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.192510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129843 restraints weight = 30666.219| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.02 r_work: 0.3328 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26388 Z= 0.137 Angle : 0.525 9.251 35770 Z= 0.271 Chirality : 0.038 0.149 4138 Planarity : 0.004 0.096 4376 Dihedral : 5.883 85.450 3454 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.36 % Allowed : 22.06 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.15), residues: 3066 helix: 2.16 (0.11), residues: 2316 sheet: -0.27 (0.40), residues: 160 loop : -1.50 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 288 TYR 0.022 0.001 TYR D 284 PHE 0.013 0.001 PHE C 735 TRP 0.049 0.002 TRP C 693 HIS 0.002 0.001 HIS C 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (26388) covalent geometry : angle 0.52459 / 0.27 (35770) hydrogen bonds : bond 0.04978 / 3.30 ( 1682) hydrogen bonds : angle 3.61359 / 2.60 ( 4989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 280 time to evaluate : 1.031 Fit side-chains REVERT: A 217 TRP cc_start: 0.7015 (t60) cc_final: 0.6771 (m-10) REVERT: A 219 MET cc_start: 0.6037 (mmt) cc_final: 0.5474 (ttt) REVERT: A 283 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7471 (mmtm) REVERT: A 533 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5954 (ptp90) REVERT: A 575 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7616 (mp0) REVERT: A 605 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7073 (mttp) REVERT: A 631 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: A 685 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 758 MET cc_start: 0.5329 (mmp) cc_final: 0.4091 (ptt) REVERT: A 964 MET cc_start: 0.6655 (ttt) cc_final: 0.5985 (mmt) REVERT: A 1011 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7053 (mt) REVERT: C 119 ARG cc_start: 0.5724 (mtm110) cc_final: 0.5353 (ptp-110) REVERT: C 126 SER cc_start: 0.8057 (p) cc_final: 0.7743 (m) REVERT: C 189 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6428 (mtm) REVERT: C 283 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7525 (mmtm) REVERT: C 378 ILE cc_start: 0.4424 (mm) cc_final: 0.3752 (pt) REVERT: C 445 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7345 (mp0) REVERT: C 533 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5813 (ptp90) REVERT: C 575 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7601 (mp0) REVERT: C 605 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7079 (mttp) REVERT: C 631 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: C 649 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7772 (mp0) REVERT: C 685 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 758 MET cc_start: 0.5342 (mmp) cc_final: 0.4112 (ptt) REVERT: C 964 MET cc_start: 0.6672 (ttt) cc_final: 0.5995 (mmt) REVERT: C 971 LEU cc_start: 0.7783 (tp) cc_final: 0.7528 (mp) REVERT: C 979 PHE cc_start: 0.7377 (t80) cc_final: 0.7159 (t80) REVERT: C 1011 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7096 (mt) REVERT: D 106 ILE cc_start: 0.6741 (mt) cc_final: 0.6443 (tt) REVERT: D 140 LYS cc_start: 0.8234 (tppt) cc_final: 0.7470 (ttpt) REVERT: D 295 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: D 353 MET cc_start: 0.6533 (mpp) cc_final: 0.6213 (mpp) REVERT: D 395 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5338 (mtpp) REVERT: D 435 GLU cc_start: 0.8114 (tp30) cc_final: 0.7715 (tp30) REVERT: D 452 ARG cc_start: 0.2429 (OUTLIER) cc_final: 0.1806 (tpm170) REVERT: D 662 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7604 (mt-10) REVERT: D 697 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6136 (mt) REVERT: D 698 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7050 (t) REVERT: D 1051 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7112 (mp0) REVERT: B 106 ILE cc_start: 0.6782 (mt) cc_final: 0.6452 (tt) REVERT: B 140 LYS cc_start: 0.8204 (tppt) cc_final: 0.7431 (ttpt) REVERT: B 295 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: B 353 MET cc_start: 0.6561 (mpp) cc_final: 0.6249 (mpp) REVERT: B 395 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5253 (mtpp) REVERT: B 435 GLU cc_start: 0.8142 (tp30) cc_final: 0.7769 (tp30) REVERT: B 574 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7303 (mptt) REVERT: B 662 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7616 (mt-10) REVERT: B 697 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6134 (mt) REVERT: B 698 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7051 (t) REVERT: B 987 GLN cc_start: 0.7839 (mm110) cc_final: 0.7528 (mp10) REVERT: B 1051 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7147 (mp0) outliers start: 92 outliers final: 58 residues processed: 350 average time/residue: 0.5685 time to fit residues: 235.8794 Evaluate side-chains 353 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 533 ARG Chi-restraints excluded: chain C residue 605 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 766 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 991 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 179 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 266 optimal weight: 0.0020 chunk 35 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 overall best weight: 2.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 765 HIS ** D 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 765 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.190519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126898 restraints weight = 30527.807| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.03 r_work: 0.3301 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26388 Z= 0.176 Angle : 0.565 10.404 35770 Z= 0.292 Chirality : 0.040 0.169 4138 Planarity : 0.004 0.093 4376 Dihedral : 6.062 84.833 3454 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.79 % Allowed : 21.81 % Favored : 74.40 % 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: 1.82 (0.15), residues: 3066 helix: 1.99 (0.11), residues: 2316 sheet: -0.25 (0.41), residues: 152 loop : -1.56 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 288 TYR 0.021 0.001 TYR D 284 PHE 0.026 0.002 PHE A 979 TRP 0.053 0.002 TRP A 693 HIS 0.009 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (26388) covalent geometry : angle 0.56492 / 0.29 (35770) hydrogen bonds : bond 0.05849 / 3.88 ( 1682) hydrogen bonds : angle 3.72849 / 2.68 ( 4989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10719.96 seconds wall clock time: 182 minutes 49.78 seconds (10969.78 seconds total)