Starting phenix.real_space_refine on Sat Aug 8 16:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnc_65207/08_2026/9vnc_65207.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 128 5.16 5 C 18452 2.51 5 N 4648 2.21 5 O 5068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 28300 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7023 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7023 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7023 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7023 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.11, per 1000 atoms: 0.22 Number of scatterers: 28300 At special positions: 0 Unit cell: (133.35, 133.35, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 128 16.00 O 5068 8.00 N 4648 7.00 C 18452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6656 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 4 sheets defined 72.5% alpha, 3.0% 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 136 removed outlier: 4.050A 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 186 through 202 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.515A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.557A pdb=" N PHE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 438 through 446 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 518 through 531 Processing helix chain 'A' and resid 559 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.684A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.566A pdb=" N VAL A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 636 removed outlier: 3.605A pdb=" N GLU A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 655 through 664 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 698 removed outlier: 3.614A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 697 " --> pdb=" O TRP A 693 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 698' Processing helix chain 'A' and resid 723 through 733 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.858A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.683A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 853 through 860 removed outlier: 3.647A pdb=" N LEU A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.523A pdb=" N ILE A 904 " --> pdb=" O PHE A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 955 through 969 Processing helix chain 'A' and resid 970 through 1009 removed outlier: 5.732A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1072 Processing helix chain 'A' and resid 1073 through 1075 No H-bonds generated for 'chain 'A' and resid 1073 through 1075' Processing helix chain 'A' and resid 1076 through 1104 removed outlier: 4.059A pdb=" N HIS A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.985A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.555A pdb=" N PHE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 518 through 531 Processing helix chain 'D' and resid 559 through 572 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.686A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 604 removed outlier: 3.588A pdb=" N VAL D 604 " --> pdb=" O THR D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 636 removed outlier: 3.605A pdb=" N GLU D 620 " --> pdb=" O GLU D 616 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 Processing helix chain 'D' and resid 655 through 664 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 698 removed outlier: 3.615A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 696 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 697 " --> pdb=" O TRP D 693 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 691 through 698' Processing helix chain 'D' and resid 723 through 733 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 818 removed outlier: 3.859A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 841 removed outlier: 3.688A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 847 Processing helix chain 'D' and resid 853 through 860 removed outlier: 3.674A pdb=" N LEU D 860 " --> pdb=" O LYS D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 955 through 969 removed outlier: 3.509A pdb=" N LEU D 959 " --> pdb=" O ILE D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 1009 removed outlier: 5.706A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D1009 " --> pdb=" O TYR D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1072 Processing helix chain 'D' and resid 1073 through 1075 No H-bonds generated for 'chain 'D' and resid 1073 through 1075' Processing helix chain 'D' and resid 1076 through 1104 removed outlier: 4.054A pdb=" N HIS D1080 " --> pdb=" O GLU D1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.983A 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 186 through 202 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.554A pdb=" N PHE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 458 through 468 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 518 through 531 Processing helix chain 'C' and resid 559 through 572 Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.682A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.586A pdb=" N VAL C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 636 removed outlier: 3.566A pdb=" N GLU C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 655 through 664 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 698 removed outlier: 3.611A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 696 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 697 " --> pdb=" O TRP C 693 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 691 through 698' Processing helix chain 'C' and resid 723 through 733 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.859A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 removed outlier: 3.686A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 841 " --> pdb=" O ILE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 853 through 860 removed outlier: 3.644A pdb=" N LEU C 860 " --> pdb=" O LYS C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.528A pdb=" N ILE C 904 " --> pdb=" O PHE C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 955 through 969 removed outlier: 3.503A pdb=" N LEU C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1009 removed outlier: 5.714A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C1009 " --> pdb=" O TYR C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1072 Processing helix chain 'C' and resid 1073 through 1075 No H-bonds generated for 'chain 'C' and resid 1073 through 1075' Processing helix chain 'C' and resid 1076 through 1104 removed outlier: 4.055A pdb=" N HIS C1080 " --> pdb=" O GLU C1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.993A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.555A pdb=" N PHE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 518 through 531 Processing helix chain 'B' and resid 559 through 572 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.687A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.581A pdb=" N VAL B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 636 removed outlier: 3.604A pdb=" N GLU B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 Processing helix chain 'B' and resid 655 through 664 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 698 removed outlier: 3.614A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 696 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 697 " --> pdb=" O TRP B 693 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 698' Processing helix chain 'B' and resid 723 through 733 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.857A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 841 removed outlier: 3.689A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 853 through 860 removed outlier: 3.701A pdb=" N LEU B 860 " --> pdb=" O LYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.506A pdb=" N ILE B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 955 through 969 Processing helix chain 'B' and resid 970 through 1009 removed outlier: 5.697A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B1009 " --> pdb=" O TYR B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1072 Processing helix chain 'B' and resid 1073 through 1075 No H-bonds generated for 'chain 'B' and resid 1073 through 1075' Processing helix chain 'B' and resid 1076 through 1104 removed outlier: 4.056A pdb=" N HIS B1080 " --> pdb=" O GLU B1076 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.875A pdb=" N LEU A 118 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 259 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 145 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE A 394 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 328 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.878A pdb=" N LEU D 118 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D 259 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA D 216 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE D 394 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL D 328 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.867A pdb=" N LEU C 118 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 259 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA C 216 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE C 394 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 328 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.893A pdb=" N LEU B 118 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 259 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE B 394 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 328 " --> pdb=" O ILE B 394 " (cutoff:3.500A) 1792 hydrogen bonds defined for protein. 5352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4508 1.30 - 1.43: 7921 1.43 - 1.56: 16339 1.56 - 1.68: 0 1.68 - 1.81: 196 Bond restraints: 28964 Sorted by residual: bond pdb=" N21 KX7 C1203 " pdb=" O22 KX7 C1203 " ideal model delta sigma weight residual 1.208 1.400 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" N21 KX7 B1203 " pdb=" O22 KX7 B1203 " ideal model delta sigma weight residual 1.208 1.400 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" N21 KX7 A1202 " pdb=" O22 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.400 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" N21 KX7 D1203 " pdb=" O22 KX7 D1203 " ideal model delta sigma weight residual 1.208 1.400 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C02 KX7 D1203 " pdb=" C03 KX7 D1203 " ideal model delta sigma weight residual 1.331 1.480 -0.149 2.00e-02 2.50e+03 5.59e+01 ... (remaining 28959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 38449 1.55 - 3.11: 657 3.11 - 4.66: 191 4.66 - 6.22: 11 6.22 - 7.77: 12 Bond angle restraints: 39320 Sorted by residual: angle pdb=" N ILE B 955 " pdb=" CA ILE B 955 " pdb=" C ILE B 955 " ideal model delta sigma weight residual 111.81 108.51 3.30 8.60e-01 1.35e+00 1.47e+01 angle pdb=" CA GLN D 306 " pdb=" CB GLN D 306 " pdb=" CG GLN D 306 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.11e+00 angle pdb=" CB GLU C 637 " pdb=" CG GLU C 637 " pdb=" CD GLU C 637 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.70e+00 3.46e-01 5.62e+00 angle pdb=" CB GLU B 637 " pdb=" CG GLU B 637 " pdb=" CD GLU B 637 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.70e+00 3.46e-01 5.54e+00 angle pdb=" CB GLU D 637 " pdb=" CG GLU D 637 " pdb=" CD GLU D 637 " ideal model delta sigma weight residual 112.60 116.56 -3.96 1.70e+00 3.46e-01 5.44e+00 ... (remaining 39315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 14339 16.16 - 32.32: 1925 32.32 - 48.48: 602 48.48 - 64.64: 179 64.64 - 80.81: 55 Dihedral angle restraints: 17100 sinusoidal: 6856 harmonic: 10244 Sorted by residual: dihedral pdb=" CA ASP B 918 " pdb=" C ASP B 918 " pdb=" N VAL B 919 " pdb=" CA VAL B 919 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP D 918 " pdb=" C ASP D 918 " pdb=" N VAL D 919 " pdb=" CA VAL D 919 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE A 904 " pdb=" C ILE A 904 " pdb=" N TYR A 905 " pdb=" CA TYR A 905 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2973 0.027 - 0.055: 961 0.055 - 0.082: 325 0.082 - 0.109: 131 0.109 - 0.137: 66 Chirality restraints: 4456 Sorted by residual: chirality pdb=" CA ILE A 146 " pdb=" N ILE A 146 " pdb=" C ILE A 146 " pdb=" CB ILE A 146 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ASN A 199 " pdb=" N ASN A 199 " pdb=" C ASN A 199 " pdb=" CB ASN A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 299 " pdb=" N ILE A 299 " pdb=" C ILE A 299 " pdb=" CB ILE A 299 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 4453 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 369 " -0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 370 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 671 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 672 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 672 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 672 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 369 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.55e+00 pdb=" N PRO C 370 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.022 5.00e-02 4.00e+02 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7075 2.79 - 3.32: 30549 3.32 - 3.85: 46986 3.85 - 4.37: 51692 4.37 - 4.90: 87055 Nonbonded interactions: 223357 Sorted by model distance: nonbonded pdb=" OE1 GLN B 785 " pdb="CA CA B1202 " model vdw 2.268 2.510 nonbonded pdb=" OE1 GLN C 785 " pdb="CA CA C1202 " model vdw 2.268 2.510 nonbonded pdb=" OE1 GLN D 785 " pdb="CA CA D1202 " model vdw 2.268 2.510 nonbonded pdb=" OE1 GLN A 785 " pdb="CA CA A1201 " model vdw 2.269 2.510 nonbonded pdb=" OD1 ASN A 799 " pdb="CA CA A1201 " model vdw 2.417 2.510 ... (remaining 223352 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 1104) selection = (chain 'B' and resid 103 through 1104) selection = (chain 'C' and resid 103 through 1104) selection = (chain 'D' and resid 103 through 1104) } 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: 2.430 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.860 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 28968 Z= 0.230 Angle : 0.558 7.769 39328 Z= 0.292 Chirality : 0.035 0.137 4456 Planarity : 0.003 0.040 4860 Dihedral : 17.196 80.806 10432 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.09 % Allowed : 19.69 % Favored : 79.21 % 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: 2.02 (0.15), residues: 3404 helix: 2.33 (0.11), residues: 2372 sheet: -2.02 (0.30), residues: 188 loop : -0.74 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.024 0.001 TYR D1005 PHE 0.012 0.001 PHE C 473 TRP 0.015 0.001 TRP C 567 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (28964) covalent geometry : angle 0.55837 / 0.29 (39320) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.39694 / 0.23 ( 8) hydrogen bonds : bond 0.11356 / 7.81 ( 1792) hydrogen bonds : angle 5.16117 / 3.72 ( 5352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 436 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8004 (mtt90) REVERT: A 402 GLU cc_start: 0.8568 (tp30) cc_final: 0.7981 (tp30) REVERT: A 477 PHE cc_start: 0.8513 (m-80) cc_final: 0.8248 (m-80) REVERT: A 480 ASN cc_start: 0.7858 (m-40) cc_final: 0.7545 (m110) REVERT: A 621 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.6798 (t80) REVERT: A 693 TRP cc_start: 0.8843 (p-90) cc_final: 0.8574 (p-90) REVERT: A 793 TYR cc_start: 0.7814 (t80) cc_final: 0.7396 (t80) REVERT: A 921 SER cc_start: 0.8295 (t) cc_final: 0.7802 (p) REVERT: A 1066 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8633 (mtmm) REVERT: D 162 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8093 (mtt90) REVERT: D 181 THR cc_start: 0.9218 (m) cc_final: 0.8945 (p) REVERT: D 356 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8793 (tp30) REVERT: D 401 ASP cc_start: 0.7413 (t70) cc_final: 0.7201 (t70) REVERT: D 402 GLU cc_start: 0.8703 (tp30) cc_final: 0.8314 (tp30) REVERT: D 477 PHE cc_start: 0.8650 (m-80) cc_final: 0.8425 (m-80) REVERT: D 621 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.6719 (t80) REVERT: D 693 TRP cc_start: 0.8851 (p-90) cc_final: 0.8585 (p-90) REVERT: D 793 TYR cc_start: 0.7840 (t80) cc_final: 0.7382 (t80) REVERT: D 797 LEU cc_start: 0.7932 (mm) cc_final: 0.7559 (pt) REVERT: D 1066 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8763 (mtmm) REVERT: C 119 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.4666 (ptm-80) REVERT: C 161 MET cc_start: 0.8384 (mmm) cc_final: 0.7817 (mmt) REVERT: C 162 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8045 (mtt90) REVERT: C 181 THR cc_start: 0.9196 (m) cc_final: 0.8919 (p) REVERT: C 304 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: C 356 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8794 (tp30) REVERT: C 402 GLU cc_start: 0.8556 (tp30) cc_final: 0.7996 (tp30) REVERT: C 621 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.6782 (t80) REVERT: C 693 TRP cc_start: 0.8834 (p-90) cc_final: 0.8568 (p-90) REVERT: C 793 TYR cc_start: 0.7866 (t80) cc_final: 0.7414 (t80) REVERT: C 1066 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8649 (mtmm) REVERT: B 161 MET cc_start: 0.8323 (mmm) cc_final: 0.7764 (mmt) REVERT: B 162 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8060 (mtt90) REVERT: B 356 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8820 (tp30) REVERT: B 402 GLU cc_start: 0.8671 (tp30) cc_final: 0.8307 (tp30) REVERT: B 621 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.6815 (t80) REVERT: B 693 TRP cc_start: 0.8865 (p-90) cc_final: 0.8593 (p-90) REVERT: B 793 TYR cc_start: 0.7813 (t80) cc_final: 0.7360 (t80) REVERT: B 1066 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8753 (mtmm) outliers start: 33 outliers final: 18 residues processed: 458 average time/residue: 0.1593 time to fit residues: 119.4737 Evaluate side-chains 432 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 621 TYR Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 621 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 915 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 438 GLN A1050 ASN D 136 HIS ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D1050 ASN C 136 HIS ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C1050 ASN B 136 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105780 restraints weight = 61635.458| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.50 r_work: 0.3366 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28968 Z= 0.172 Angle : 0.558 8.392 39328 Z= 0.296 Chirality : 0.039 0.157 4456 Planarity : 0.004 0.041 4860 Dihedral : 5.974 60.716 4057 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.38 % Allowed : 18.90 % Favored : 77.72 % 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: 1.87 (0.14), residues: 3404 helix: 2.19 (0.11), residues: 2384 sheet: -1.89 (0.31), residues: 188 loop : -0.83 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1008 TYR 0.011 0.001 TYR A1005 PHE 0.014 0.001 PHE C 779 TRP 0.014 0.001 TRP D 567 HIS 0.004 0.001 HIS D 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (28964) covalent geometry : angle 0.55755 / 0.30 (39320) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.32972 / 0.19 ( 8) hydrogen bonds : bond 0.04749 / 3.19 ( 1792) hydrogen bonds : angle 4.31269 / 3.08 ( 5352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 445 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8001 (mtt90) REVERT: A 480 ASN cc_start: 0.7853 (m-40) cc_final: 0.7504 (m110) REVERT: A 693 TRP cc_start: 0.8835 (p-90) cc_final: 0.8542 (p-90) REVERT: A 797 LEU cc_start: 0.8150 (mm) cc_final: 0.7665 (pt) REVERT: A 920 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: A 1056 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8550 (tm-30) REVERT: A 1066 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8778 (tppt) REVERT: D 119 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.4887 (ptm-80) REVERT: D 181 THR cc_start: 0.9170 (m) cc_final: 0.8886 (p) REVERT: D 401 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7421 (t70) REVERT: D 402 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8446 (tp30) REVERT: D 477 PHE cc_start: 0.8632 (m-10) cc_final: 0.8393 (m-80) REVERT: D 480 ASN cc_start: 0.7598 (m-40) cc_final: 0.7285 (m110) REVERT: D 693 TRP cc_start: 0.8863 (p-90) cc_final: 0.8556 (p-90) REVERT: D 797 LEU cc_start: 0.8164 (mm) cc_final: 0.7684 (pt) REVERT: D 924 TYR cc_start: 0.4931 (t80) cc_final: 0.4606 (t80) REVERT: D 1056 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: D 1066 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8790 (tppt) REVERT: C 119 ARG cc_start: 0.5219 (OUTLIER) cc_final: 0.4987 (ptt-90) REVERT: C 162 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8065 (mtt90) REVERT: C 181 THR cc_start: 0.9170 (m) cc_final: 0.8890 (p) REVERT: C 480 ASN cc_start: 0.7574 (m-40) cc_final: 0.7244 (m110) REVERT: C 693 TRP cc_start: 0.8860 (p-90) cc_final: 0.8553 (p-90) REVERT: C 797 LEU cc_start: 0.8156 (mm) cc_final: 0.7673 (pt) REVERT: C 924 TYR cc_start: 0.4892 (t80) cc_final: 0.4566 (t80) REVERT: C 1056 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8548 (tm-30) REVERT: C 1066 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8806 (tppt) REVERT: B 161 MET cc_start: 0.8347 (mmm) cc_final: 0.7854 (mmt) REVERT: B 162 ARG cc_start: 0.8454 (mtt180) cc_final: 0.8042 (mtt90) REVERT: B 402 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: B 462 MET cc_start: 0.9060 (tpt) cc_final: 0.8549 (tpp) REVERT: B 507 ARG cc_start: 0.8598 (mpt180) cc_final: 0.8338 (mpt180) REVERT: B 693 TRP cc_start: 0.8864 (p-90) cc_final: 0.8555 (p-90) REVERT: B 797 LEU cc_start: 0.8162 (mm) cc_final: 0.7680 (pt) REVERT: B 924 TYR cc_start: 0.4832 (t80) cc_final: 0.4546 (t80) REVERT: B 1056 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: B 1066 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8776 (tppt) outliers start: 102 outliers final: 61 residues processed: 513 average time/residue: 0.1586 time to fit residues: 131.7368 Evaluate side-chains 464 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 393 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 1056 GLU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1056 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 225 optimal weight: 0.0000 chunk 299 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 249 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 210 optimal weight: 9.9990 chunk 303 optimal weight: 7.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.149942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112122 restraints weight = 62199.732| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.56 r_work: 0.3441 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28968 Z= 0.110 Angle : 0.504 7.507 39328 Z= 0.266 Chirality : 0.037 0.137 4456 Planarity : 0.004 0.042 4860 Dihedral : 5.072 57.660 4027 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 20.06 % Favored : 77.45 % 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 (0.14), residues: 3404 helix: 2.35 (0.11), residues: 2380 sheet: -1.61 (0.32), residues: 196 loop : -0.86 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 360 TYR 0.020 0.001 TYR B 793 PHE 0.014 0.001 PHE C 926 TRP 0.015 0.001 TRP C 994 HIS 0.002 0.000 HIS B 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (28964) covalent geometry : angle 0.50393 / 0.27 (39320) SS BOND : bond 0.00124 / 0.06 ( 4) SS BOND : angle 0.67554 / 0.40 ( 8) hydrogen bonds : bond 0.03823 / 2.57 ( 1792) hydrogen bonds : angle 3.94940 / 2.80 ( 5352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 479 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7908 (mtt90) REVERT: A 219 MET cc_start: 0.7319 (mmm) cc_final: 0.6366 (tpp) REVERT: A 480 ASN cc_start: 0.7783 (m-40) cc_final: 0.7452 (m110) REVERT: A 693 TRP cc_start: 0.8856 (p-90) cc_final: 0.8544 (p-90) REVERT: A 793 TYR cc_start: 0.7700 (t80) cc_final: 0.6898 (t80) REVERT: A 920 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: A 921 SER cc_start: 0.8327 (t) cc_final: 0.7838 (p) REVERT: A 1056 GLU cc_start: 0.8789 (tt0) cc_final: 0.8570 (tm-30) REVERT: D 162 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.8194 (mtt90) REVERT: D 219 MET cc_start: 0.6851 (mmm) cc_final: 0.6582 (tpp) REVERT: D 633 TYR cc_start: 0.8814 (t80) cc_final: 0.8570 (t80) REVERT: D 693 TRP cc_start: 0.8839 (p-90) cc_final: 0.8559 (p-90) REVERT: D 793 TYR cc_start: 0.7673 (t80) cc_final: 0.6942 (t80) REVERT: D 851 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7716 (ptp90) REVERT: D 1056 GLU cc_start: 0.8764 (tt0) cc_final: 0.8553 (tm-30) REVERT: C 162 ARG cc_start: 0.8456 (mtt180) cc_final: 0.7983 (mtt90) REVERT: C 219 MET cc_start: 0.6896 (mmm) cc_final: 0.6599 (tpp) REVERT: C 401 ASP cc_start: 0.7776 (t70) cc_final: 0.7393 (t0) REVERT: C 633 TYR cc_start: 0.8819 (t80) cc_final: 0.8577 (t80) REVERT: C 693 TRP cc_start: 0.8835 (p-90) cc_final: 0.8548 (p-90) REVERT: C 793 TYR cc_start: 0.7691 (t80) cc_final: 0.6891 (t80) REVERT: C 1056 GLU cc_start: 0.8810 (tt0) cc_final: 0.8601 (tm-30) REVERT: B 119 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.5087 (ptt-90) REVERT: B 161 MET cc_start: 0.8230 (mmm) cc_final: 0.7715 (mmt) REVERT: B 162 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8030 (mtt90) REVERT: B 219 MET cc_start: 0.6864 (mmm) cc_final: 0.6581 (tpp) REVERT: B 401 ASP cc_start: 0.7540 (t70) cc_final: 0.7043 (t0) REVERT: B 402 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: B 462 MET cc_start: 0.9075 (tpt) cc_final: 0.8589 (tpp) REVERT: B 633 TYR cc_start: 0.8821 (t80) cc_final: 0.8587 (t80) REVERT: B 693 TRP cc_start: 0.8839 (p-90) cc_final: 0.8550 (p-90) REVERT: B 851 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7704 (ptp90) REVERT: B 1056 GLU cc_start: 0.8794 (tt0) cc_final: 0.8581 (tm-30) REVERT: B 1066 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8809 (tppt) outliers start: 75 outliers final: 35 residues processed: 521 average time/residue: 0.1612 time to fit residues: 136.3762 Evaluate side-chains 461 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 421 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 930 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 250 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN A 438 GLN A 928 HIS ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 438 GLN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 406 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.141661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102858 restraints weight = 62365.404| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.51 r_work: 0.3341 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28968 Z= 0.233 Angle : 0.600 5.882 39328 Z= 0.321 Chirality : 0.041 0.148 4456 Planarity : 0.004 0.044 4860 Dihedral : 5.562 61.072 4018 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.44 % Allowed : 20.16 % Favored : 75.40 % 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: 1.65 (0.14), residues: 3404 helix: 2.04 (0.10), residues: 2384 sheet: -1.69 (0.31), residues: 196 loop : -1.02 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 470 TYR 0.026 0.002 TYR B 793 PHE 0.021 0.002 PHE D 926 TRP 0.015 0.002 TRP C 567 HIS 0.004 0.001 HIS C 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (28964) covalent geometry : angle 0.60005 / 0.32 (39320) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 0.54925 / 0.33 ( 8) hydrogen bonds : bond 0.05020 / 3.37 ( 1792) hydrogen bonds : angle 4.30059 / 3.07 ( 5352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 410 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.5286 (ptt-90) REVERT: A 155 PHE cc_start: 0.6724 (m-10) cc_final: 0.6418 (m-10) REVERT: A 181 THR cc_start: 0.9002 (m) cc_final: 0.8700 (p) REVERT: A 480 ASN cc_start: 0.7824 (m-40) cc_final: 0.7511 (m110) REVERT: A 693 TRP cc_start: 0.8827 (p-90) cc_final: 0.8550 (p-90) REVERT: A 920 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: D 155 PHE cc_start: 0.6677 (m-10) cc_final: 0.6268 (m-10) REVERT: D 181 THR cc_start: 0.9115 (m) cc_final: 0.8816 (p) REVERT: D 219 MET cc_start: 0.6836 (mmm) cc_final: 0.6498 (tpp) REVERT: D 401 ASP cc_start: 0.7950 (t70) cc_final: 0.7714 (t70) REVERT: D 402 GLU cc_start: 0.8954 (mp0) cc_final: 0.8655 (tt0) REVERT: D 693 TRP cc_start: 0.8862 (p-90) cc_final: 0.8597 (p-90) REVERT: D 920 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: C 155 PHE cc_start: 0.6705 (m-10) cc_final: 0.6292 (m-10) REVERT: C 162 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7989 (mtt-85) REVERT: C 181 THR cc_start: 0.9119 (m) cc_final: 0.8818 (p) REVERT: C 219 MET cc_start: 0.6869 (mmm) cc_final: 0.6499 (tpp) REVERT: C 445 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7828 (mm-30) REVERT: C 693 TRP cc_start: 0.8862 (p-90) cc_final: 0.8599 (p-90) REVERT: B 155 PHE cc_start: 0.6677 (m-10) cc_final: 0.6302 (m-10) REVERT: B 162 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7967 (mtt90) REVERT: B 181 THR cc_start: 0.9118 (m) cc_final: 0.8774 (p) REVERT: B 219 MET cc_start: 0.6936 (mmm) cc_final: 0.6574 (tpp) REVERT: B 401 ASP cc_start: 0.7627 (t70) cc_final: 0.7167 (t0) REVERT: B 402 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (tp30) REVERT: B 445 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 477 PHE cc_start: 0.8697 (m-80) cc_final: 0.8491 (m-80) REVERT: B 693 TRP cc_start: 0.8843 (p-90) cc_final: 0.8574 (p-90) REVERT: B 920 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: B 1066 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8830 (tppt) outliers start: 134 outliers final: 94 residues processed: 496 average time/residue: 0.1465 time to fit residues: 119.6454 Evaluate side-chains 480 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 381 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 920 ASP Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 249 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN A 438 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 438 GLN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.147396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.109832 restraints weight = 62243.999| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.51 r_work: 0.3391 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28968 Z= 0.127 Angle : 0.520 6.098 39328 Z= 0.278 Chirality : 0.038 0.137 4456 Planarity : 0.004 0.046 4860 Dihedral : 5.182 59.069 4018 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.98 % Allowed : 22.88 % Favored : 74.14 % 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: 1.84 (0.14), residues: 3404 helix: 2.19 (0.11), residues: 2384 sheet: -1.56 (0.32), residues: 196 loop : -0.99 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 119 TYR 0.024 0.001 TYR A 793 PHE 0.016 0.001 PHE C 779 TRP 0.017 0.001 TRP B 994 HIS 0.005 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (28964) covalent geometry : angle 0.51996 / 0.28 (39320) SS BOND : bond 0.00094 / 0.05 ( 4) SS BOND : angle 0.68600 / 0.40 ( 8) hydrogen bonds : bond 0.04209 / 2.81 ( 1792) hydrogen bonds : angle 3.98049 / 2.83 ( 5352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 436 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.5374 (ptt-90) REVERT: A 155 PHE cc_start: 0.6508 (m-10) cc_final: 0.6206 (m-10) REVERT: A 181 THR cc_start: 0.9048 (m) cc_final: 0.8714 (p) REVERT: A 480 ASN cc_start: 0.7763 (m-40) cc_final: 0.7469 (m110) REVERT: A 693 TRP cc_start: 0.8840 (p-90) cc_final: 0.8542 (p-90) REVERT: A 863 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6733 (pmt) REVERT: A 920 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: D 155 PHE cc_start: 0.6643 (m-10) cc_final: 0.6408 (m-10) REVERT: D 181 THR cc_start: 0.9113 (m) cc_final: 0.8765 (p) REVERT: D 219 MET cc_start: 0.6817 (mmm) cc_final: 0.6564 (tpp) REVERT: D 401 ASP cc_start: 0.7995 (t70) cc_final: 0.7759 (t70) REVERT: D 402 GLU cc_start: 0.8939 (mp0) cc_final: 0.8618 (tt0) REVERT: D 462 MET cc_start: 0.9146 (tpt) cc_final: 0.8908 (tpt) REVERT: D 693 TRP cc_start: 0.8862 (p-90) cc_final: 0.8580 (p-90) REVERT: C 155 PHE cc_start: 0.6707 (m-10) cc_final: 0.6465 (m-10) REVERT: C 162 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8124 (mtt90) REVERT: C 181 THR cc_start: 0.9123 (m) cc_final: 0.8776 (p) REVERT: C 219 MET cc_start: 0.6772 (mmm) cc_final: 0.6476 (tpp) REVERT: C 401 ASP cc_start: 0.7854 (t70) cc_final: 0.7476 (t0) REVERT: C 693 TRP cc_start: 0.8860 (p-90) cc_final: 0.8584 (p-90) REVERT: C 863 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6580 (pmt) REVERT: C 947 ASN cc_start: 0.8363 (m-40) cc_final: 0.8082 (t0) REVERT: C 1056 GLU cc_start: 0.8904 (tt0) cc_final: 0.8698 (tm-30) REVERT: B 155 PHE cc_start: 0.6573 (m-10) cc_final: 0.6234 (m-10) REVERT: B 162 ARG cc_start: 0.8485 (mtt180) cc_final: 0.7965 (mtt90) REVERT: B 181 THR cc_start: 0.9054 (m) cc_final: 0.8683 (p) REVERT: B 219 MET cc_start: 0.6723 (mmm) cc_final: 0.6430 (tpp) REVERT: B 304 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: B 402 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: B 693 TRP cc_start: 0.8863 (p-90) cc_final: 0.8606 (p-90) REVERT: B 793 TYR cc_start: 0.7650 (t80) cc_final: 0.7038 (t80) REVERT: B 1056 GLU cc_start: 0.8904 (tt0) cc_final: 0.8688 (tm-30) REVERT: B 1066 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8827 (tppt) outliers start: 90 outliers final: 58 residues processed: 491 average time/residue: 0.1514 time to fit residues: 123.1532 Evaluate side-chains 455 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 391 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 0.0000 chunk 171 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 331 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 438 GLN C 973 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111024 restraints weight = 62403.759| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.52 r_work: 0.3492 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28968 Z= 0.118 Angle : 0.518 10.775 39328 Z= 0.274 Chirality : 0.037 0.176 4456 Planarity : 0.004 0.044 4860 Dihedral : 5.023 58.256 4018 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.12 % Allowed : 23.24 % Favored : 73.64 % 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 (0.14), residues: 3404 helix: 2.21 (0.11), residues: 2384 sheet: -1.44 (0.32), residues: 196 loop : -0.81 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 360 TYR 0.025 0.001 TYR C 793 PHE 0.021 0.001 PHE D 874 TRP 0.016 0.001 TRP B 567 HIS 0.004 0.000 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (28964) covalent geometry : angle 0.51792 / 0.27 (39320) SS BOND : bond 0.00101 / 0.05 ( 4) SS BOND : angle 0.62602 / 0.37 ( 8) hydrogen bonds : bond 0.03941 / 2.64 ( 1792) hydrogen bonds : angle 3.88214 / 2.75 ( 5352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 415 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5625 (ptt-90) REVERT: A 155 PHE cc_start: 0.6730 (m-10) cc_final: 0.6416 (m-10) REVERT: A 181 THR cc_start: 0.9055 (m) cc_final: 0.8676 (p) REVERT: A 480 ASN cc_start: 0.7746 (m-40) cc_final: 0.7446 (m110) REVERT: A 627 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8204 (mt-10) REVERT: A 693 TRP cc_start: 0.8859 (p-90) cc_final: 0.8560 (p-90) REVERT: A 920 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: A 1056 GLU cc_start: 0.9054 (tt0) cc_final: 0.8821 (tm-30) REVERT: D 155 PHE cc_start: 0.6775 (m-10) cc_final: 0.6520 (m-10) REVERT: D 181 THR cc_start: 0.9125 (m) cc_final: 0.8775 (p) REVERT: D 219 MET cc_start: 0.6760 (mmm) cc_final: 0.6542 (tpp) REVERT: D 304 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: D 401 ASP cc_start: 0.7947 (t70) cc_final: 0.7464 (t0) REVERT: D 402 GLU cc_start: 0.8916 (mp0) cc_final: 0.8581 (tt0) REVERT: D 462 MET cc_start: 0.9153 (tpt) cc_final: 0.8925 (tpt) REVERT: D 480 ASN cc_start: 0.7832 (m-40) cc_final: 0.7629 (m-40) REVERT: D 627 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8237 (mt-10) REVERT: D 693 TRP cc_start: 0.8887 (p-90) cc_final: 0.8598 (p-90) REVERT: D 793 TYR cc_start: 0.7558 (t80) cc_final: 0.6983 (t80) REVERT: C 155 PHE cc_start: 0.6733 (m-10) cc_final: 0.6403 (m-10) REVERT: C 162 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7538 (mtt-85) REVERT: C 181 THR cc_start: 0.9137 (m) cc_final: 0.8787 (p) REVERT: C 199 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 219 MET cc_start: 0.6795 (mmm) cc_final: 0.6545 (tpp) REVERT: C 401 ASP cc_start: 0.7864 (t70) cc_final: 0.7531 (t0) REVERT: C 480 ASN cc_start: 0.7569 (m-40) cc_final: 0.7304 (m110) REVERT: C 627 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8247 (mt-10) REVERT: C 693 TRP cc_start: 0.8867 (p-90) cc_final: 0.8584 (p-90) REVERT: C 793 TYR cc_start: 0.7561 (t80) cc_final: 0.6894 (t80) REVERT: C 947 ASN cc_start: 0.8353 (m-40) cc_final: 0.8061 (t0) REVERT: B 155 PHE cc_start: 0.6722 (m-10) cc_final: 0.6363 (m-10) REVERT: B 162 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8071 (mtt90) REVERT: B 181 THR cc_start: 0.9058 (m) cc_final: 0.8677 (p) REVERT: B 219 MET cc_start: 0.6759 (mmm) cc_final: 0.6517 (tpp) REVERT: B 304 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 401 ASP cc_start: 0.7569 (t70) cc_final: 0.7172 (t0) REVERT: B 402 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: B 627 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8229 (mt-10) REVERT: B 693 TRP cc_start: 0.8845 (p-90) cc_final: 0.8604 (p-90) outliers start: 94 outliers final: 72 residues processed: 482 average time/residue: 0.1493 time to fit residues: 118.7177 Evaluate side-chains 479 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 155 optimal weight: 0.9990 chunk 345 optimal weight: 30.0000 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 20.0000 chunk 347 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.147110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110164 restraints weight = 62212.174| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.46 r_work: 0.3385 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28968 Z= 0.141 Angle : 0.546 12.130 39328 Z= 0.285 Chirality : 0.038 0.166 4456 Planarity : 0.004 0.042 4860 Dihedral : 4.954 59.754 4012 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.75 % Allowed : 23.21 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.14), residues: 3404 helix: 2.19 (0.11), residues: 2384 sheet: -1.40 (0.32), residues: 196 loop : -0.85 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 360 TYR 0.028 0.001 TYR B 793 PHE 0.026 0.001 PHE D 874 TRP 0.017 0.001 TRP B 567 HIS 0.003 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (28964) covalent geometry : angle 0.54613 / 0.29 (39320) SS BOND : bond 0.00036 / 0.02 ( 4) SS BOND : angle 0.57000 / 0.34 ( 8) hydrogen bonds : bond 0.04144 / 2.78 ( 1792) hydrogen bonds : angle 3.93809 / 2.79 ( 5352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 414 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5699 (ptt-90) REVERT: A 155 PHE cc_start: 0.6772 (m-10) cc_final: 0.6514 (m-10) REVERT: A 304 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: A 452 ARG cc_start: 0.6768 (mmp80) cc_final: 0.6560 (mmp80) REVERT: A 480 ASN cc_start: 0.7743 (m-40) cc_final: 0.7443 (m110) REVERT: A 638 ASP cc_start: 0.7994 (t0) cc_final: 0.7784 (t0) REVERT: A 693 TRP cc_start: 0.8856 (p-90) cc_final: 0.8598 (p-90) REVERT: A 793 TYR cc_start: 0.8243 (t80) cc_final: 0.7810 (t80) REVERT: A 920 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: D 155 PHE cc_start: 0.6699 (m-10) cc_final: 0.6412 (m-10) REVERT: D 181 THR cc_start: 0.9051 (m) cc_final: 0.8749 (p) REVERT: D 219 MET cc_start: 0.6798 (mmm) cc_final: 0.6570 (tpp) REVERT: D 304 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: D 401 ASP cc_start: 0.7939 (t70) cc_final: 0.7485 (t0) REVERT: D 402 GLU cc_start: 0.8923 (mp0) cc_final: 0.8596 (tt0) REVERT: D 462 MET cc_start: 0.9167 (tpt) cc_final: 0.8928 (tpt) REVERT: D 480 ASN cc_start: 0.7823 (m-40) cc_final: 0.7507 (m110) REVERT: D 638 ASP cc_start: 0.8030 (t0) cc_final: 0.7797 (t0) REVERT: D 693 TRP cc_start: 0.8880 (p-90) cc_final: 0.8636 (p-90) REVERT: C 162 ARG cc_start: 0.8364 (mtt180) cc_final: 0.7507 (mtt-85) REVERT: C 181 THR cc_start: 0.9077 (m) cc_final: 0.8776 (p) REVERT: C 199 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7359 (t0) REVERT: C 219 MET cc_start: 0.6863 (mmm) cc_final: 0.6602 (tpp) REVERT: C 304 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: C 445 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 480 ASN cc_start: 0.7607 (m-40) cc_final: 0.7289 (m110) REVERT: C 638 ASP cc_start: 0.8026 (t0) cc_final: 0.7774 (t0) REVERT: C 693 TRP cc_start: 0.8867 (p-90) cc_final: 0.8631 (p-90) REVERT: B 155 PHE cc_start: 0.6760 (m-10) cc_final: 0.6471 (m-10) REVERT: B 162 ARG cc_start: 0.8412 (mtt180) cc_final: 0.7591 (mtt-85) REVERT: B 219 MET cc_start: 0.6824 (mmm) cc_final: 0.6566 (tpp) REVERT: B 304 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 361 PHE cc_start: 0.7854 (m-80) cc_final: 0.7571 (m-80) REVERT: B 402 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: B 638 ASP cc_start: 0.8035 (t0) cc_final: 0.7782 (t0) REVERT: B 793 TYR cc_start: 0.7636 (t80) cc_final: 0.7146 (t80) outliers start: 113 outliers final: 86 residues processed: 485 average time/residue: 0.1587 time to fit residues: 127.7411 Evaluate side-chains 488 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 394 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 220 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 199 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107646 restraints weight = 62763.140| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.48 r_work: 0.3375 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28968 Z= 0.156 Angle : 0.562 11.606 39328 Z= 0.294 Chirality : 0.039 0.143 4456 Planarity : 0.004 0.049 4860 Dihedral : 5.029 60.207 4012 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.68 % Allowed : 23.71 % Favored : 72.61 % 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: 1.83 (0.14), residues: 3404 helix: 2.13 (0.11), residues: 2384 sheet: -1.38 (0.33), residues: 196 loop : -0.88 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 360 TYR 0.030 0.001 TYR D 793 PHE 0.023 0.001 PHE B 874 TRP 0.046 0.001 TRP B 693 HIS 0.003 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (28964) covalent geometry : angle 0.56187 / 0.29 (39320) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.58105 / 0.34 ( 8) hydrogen bonds : bond 0.04323 / 2.89 ( 1792) hydrogen bonds : angle 3.99103 / 2.84 ( 5352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 400 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5753 (ptt-90) REVERT: A 155 PHE cc_start: 0.6785 (m-10) cc_final: 0.6527 (m-10) REVERT: A 181 THR cc_start: 0.9053 (m) cc_final: 0.8721 (p) REVERT: A 480 ASN cc_start: 0.7722 (m-40) cc_final: 0.7412 (m110) REVERT: A 598 LEU cc_start: 0.8660 (mt) cc_final: 0.8452 (mt) REVERT: A 638 ASP cc_start: 0.8213 (t0) cc_final: 0.7963 (t0) REVERT: A 693 TRP cc_start: 0.8875 (p-90) cc_final: 0.8605 (p-90) REVERT: A 920 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: D 155 PHE cc_start: 0.6855 (m-10) cc_final: 0.6637 (m-10) REVERT: D 181 THR cc_start: 0.9119 (m) cc_final: 0.8816 (p) REVERT: D 219 MET cc_start: 0.6974 (mmm) cc_final: 0.6760 (tpp) REVERT: D 304 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: D 361 PHE cc_start: 0.7840 (m-80) cc_final: 0.7619 (m-80) REVERT: D 401 ASP cc_start: 0.7988 (t70) cc_final: 0.7535 (t0) REVERT: D 402 GLU cc_start: 0.8941 (mp0) cc_final: 0.8619 (tt0) REVERT: D 480 ASN cc_start: 0.7801 (m-40) cc_final: 0.7514 (m110) REVERT: D 638 ASP cc_start: 0.8090 (t0) cc_final: 0.7873 (t0) REVERT: D 693 TRP cc_start: 0.8866 (p-90) cc_final: 0.8632 (p-90) REVERT: D 793 TYR cc_start: 0.7639 (t80) cc_final: 0.7238 (t80) REVERT: C 162 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7650 (mtt90) REVERT: C 181 THR cc_start: 0.9140 (m) cc_final: 0.8835 (p) REVERT: C 219 MET cc_start: 0.6828 (mmm) cc_final: 0.6579 (tpp) REVERT: C 304 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: C 445 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 598 LEU cc_start: 0.8697 (mt) cc_final: 0.8482 (mt) REVERT: C 633 TYR cc_start: 0.8891 (t80) cc_final: 0.8633 (t80) REVERT: C 638 ASP cc_start: 0.8072 (t0) cc_final: 0.7859 (t0) REVERT: C 693 TRP cc_start: 0.8875 (p-90) cc_final: 0.8618 (p-90) REVERT: C 793 TYR cc_start: 0.7649 (t80) cc_final: 0.7247 (t80) REVERT: B 155 PHE cc_start: 0.6750 (m-10) cc_final: 0.6417 (m-10) REVERT: B 162 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7571 (mtt-85) REVERT: B 181 THR cc_start: 0.9025 (m) cc_final: 0.8690 (p) REVERT: B 199 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 304 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: B 402 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8312 (tp30) REVERT: B 633 TYR cc_start: 0.8893 (t80) cc_final: 0.8651 (t80) REVERT: B 638 ASP cc_start: 0.8069 (t0) cc_final: 0.7855 (t0) REVERT: B 793 TYR cc_start: 0.7658 (t80) cc_final: 0.7012 (t80) outliers start: 111 outliers final: 94 residues processed: 472 average time/residue: 0.1523 time to fit residues: 119.6845 Evaluate side-chains 487 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 386 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 18 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.143970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105900 restraints weight = 62602.370| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.51 r_work: 0.3335 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28968 Z= 0.197 Angle : 0.603 11.385 39328 Z= 0.318 Chirality : 0.040 0.144 4456 Planarity : 0.004 0.048 4860 Dihedral : 5.239 61.209 4012 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.24 % Allowed : 23.64 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3404 helix: 2.00 (0.10), residues: 2388 sheet: -1.39 (0.33), residues: 196 loop : -0.93 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 167 TYR 0.028 0.002 TYR C 793 PHE 0.023 0.002 PHE A 874 TRP 0.027 0.002 TRP B 693 HIS 0.004 0.001 HIS B 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (28964) covalent geometry : angle 0.60345 / 0.32 (39320) SS BOND : bond 0.00050 / 0.03 ( 4) SS BOND : angle 0.58519 / 0.35 ( 8) hydrogen bonds : bond 0.04703 / 3.15 ( 1792) hydrogen bonds : angle 4.12907 / 2.95 ( 5352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 403 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.6767 (m-10) cc_final: 0.6553 (m-10) REVERT: A 181 THR cc_start: 0.8999 (m) cc_final: 0.8678 (p) REVERT: A 304 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: A 480 ASN cc_start: 0.7826 (m-40) cc_final: 0.7519 (m110) REVERT: A 638 ASP cc_start: 0.8170 (t0) cc_final: 0.7958 (t0) REVERT: A 693 TRP cc_start: 0.8847 (p-90) cc_final: 0.8612 (p-90) REVERT: A 789 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (t0) REVERT: A 920 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8529 (m-30) REVERT: D 181 THR cc_start: 0.9087 (m) cc_final: 0.8825 (p) REVERT: D 304 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: D 401 ASP cc_start: 0.7981 (t70) cc_final: 0.7518 (t0) REVERT: D 402 GLU cc_start: 0.8959 (mp0) cc_final: 0.8647 (tt0) REVERT: D 638 ASP cc_start: 0.8200 (t0) cc_final: 0.7960 (t0) REVERT: D 693 TRP cc_start: 0.8855 (p-90) cc_final: 0.8652 (p-90) REVERT: D 964 MET cc_start: 0.9180 (mmm) cc_final: 0.8877 (tpt) REVERT: C 162 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7693 (mtt90) REVERT: C 181 THR cc_start: 0.9095 (m) cc_final: 0.8818 (p) REVERT: C 304 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: C 633 TYR cc_start: 0.8930 (t80) cc_final: 0.8589 (t80) REVERT: B 162 ARG cc_start: 0.8377 (mtt180) cc_final: 0.7557 (mtt-85) REVERT: B 181 THR cc_start: 0.8966 (m) cc_final: 0.8646 (p) REVERT: B 304 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 402 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8344 (tp30) REVERT: B 633 TYR cc_start: 0.8931 (t80) cc_final: 0.8600 (t80) outliers start: 128 outliers final: 104 residues processed: 488 average time/residue: 0.1680 time to fit residues: 136.5117 Evaluate side-chains 493 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 382 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 328 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.147731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110377 restraints weight = 61887.947| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.51 r_work: 0.3395 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28968 Z= 0.122 Angle : 0.564 11.778 39328 Z= 0.294 Chirality : 0.038 0.137 4456 Planarity : 0.004 0.051 4860 Dihedral : 4.975 58.694 4012 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.05 % Allowed : 25.33 % Favored : 71.62 % 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: 1.90 (0.15), residues: 3404 helix: 2.17 (0.11), residues: 2384 sheet: -1.27 (0.34), residues: 196 loop : -0.83 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 360 TYR 0.027 0.001 TYR B 793 PHE 0.024 0.001 PHE A 874 TRP 0.050 0.001 TRP C 693 HIS 0.006 0.001 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (28964) covalent geometry : angle 0.56378 / 0.29 (39320) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 0.79044 / 0.47 ( 8) hydrogen bonds : bond 0.03959 / 2.65 ( 1792) hydrogen bonds : angle 3.90284 / 2.77 ( 5352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 433 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 THR cc_start: 0.9010 (m) cc_final: 0.8681 (p) REVERT: A 304 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: A 480 ASN cc_start: 0.7737 (m-40) cc_final: 0.7397 (m110) REVERT: A 638 ASP cc_start: 0.8038 (t0) cc_final: 0.7830 (t0) REVERT: A 693 TRP cc_start: 0.8871 (p-90) cc_final: 0.8637 (p-90) REVERT: A 920 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: A 1059 MET cc_start: 0.8954 (mmt) cc_final: 0.8564 (mmt) REVERT: D 181 THR cc_start: 0.9041 (m) cc_final: 0.8744 (p) REVERT: D 304 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: D 402 GLU cc_start: 0.8945 (mp0) cc_final: 0.8621 (tt0) REVERT: D 480 ASN cc_start: 0.8080 (m-40) cc_final: 0.7828 (m110) REVERT: D 638 ASP cc_start: 0.8249 (t0) cc_final: 0.7967 (t0) REVERT: D 964 MET cc_start: 0.9165 (mmm) cc_final: 0.8853 (tpt) REVERT: D 1059 MET cc_start: 0.8951 (mmt) cc_final: 0.8547 (mmt) REVERT: C 162 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7659 (mtt90) REVERT: C 181 THR cc_start: 0.9065 (m) cc_final: 0.8754 (p) REVERT: C 480 ASN cc_start: 0.7712 (m-40) cc_final: 0.7478 (m110) REVERT: C 633 TYR cc_start: 0.8840 (t80) cc_final: 0.8607 (t80) REVERT: C 964 MET cc_start: 0.9151 (mmm) cc_final: 0.8839 (tpt) REVERT: C 1059 MET cc_start: 0.8927 (mmt) cc_final: 0.8483 (mmt) REVERT: B 162 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7705 (mtt90) REVERT: B 181 THR cc_start: 0.8970 (m) cc_final: 0.8647 (p) REVERT: B 199 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7702 (t0) REVERT: B 304 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: B 402 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: B 633 TYR cc_start: 0.8839 (t80) cc_final: 0.8615 (t80) outliers start: 92 outliers final: 81 residues processed: 493 average time/residue: 0.1689 time to fit residues: 138.3711 Evaluate side-chains 489 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 402 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 863 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 932 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 932 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 932 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 294 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 134 optimal weight: 0.0980 chunk 326 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 192 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.152939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117458 restraints weight = 58791.975| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.35 r_work: 0.3548 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28968 Z= 0.113 Angle : 0.571 13.646 39328 Z= 0.297 Chirality : 0.038 0.204 4456 Planarity : 0.005 0.196 4860 Dihedral : 4.824 55.764 4012 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.35 % Allowed : 26.09 % Favored : 71.55 % 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: 2.00 (0.15), residues: 3404 helix: 2.25 (0.11), residues: 2388 sheet: -1.07 (0.35), residues: 196 loop : -0.88 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 360 TYR 0.038 0.001 TYR D 793 PHE 0.026 0.001 PHE A 874 TRP 0.052 0.002 TRP D 693 HIS 0.006 0.000 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (28964) covalent geometry : angle 0.57141 / 0.30 (39320) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 0.80619 / 0.48 ( 8) hydrogen bonds : bond 0.03579 / 2.40 ( 1792) hydrogen bonds : angle 3.78098 / 2.68 ( 5352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6518.96 seconds wall clock time: 112 minutes 25.91 seconds (6745.91 seconds total)