Starting phenix.real_space_refine on Thu Mar 5 10:55:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.map" model { file = "/net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tge_25880/03_2026/7tge_25880.cif" } resolution = 3.68 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= -0.002 sd= 0.139 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: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 13695 2.51 5 N 3504 2.21 5 O 4169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21461 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8076 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6562 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 803} Chain breaks: 8 Chain: "C" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6263 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 767} Chain breaks: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.28, per 1000 atoms: 0.20 Number of scatterers: 21461 At special positions: 0 Unit cell: (129.6, 132.84, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 4169 8.00 N 3504 7.00 C 13695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 282 " " NAG A1203 " - " ASN A 331 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 234 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 165 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 616 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1098 " " NAG B1207 " - " ASN B 122 " " NAG B1208 " - " ASN B1134 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 709 " " NAG C1205 " - " ASN C 801 " " NAG C1206 " - " ASN C1098 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 165 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 717 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 27.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.579A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.052A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.144A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.167A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 629 through 632 removed outlier: 3.835A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.565A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.634A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.699A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.627A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 4.507A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.560A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.652A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.073A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.953A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.652A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.789A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.964A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.532A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.712A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.904A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.800A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.535A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.841A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.702A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.462A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.717A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.887A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.481A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.021A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.140A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.867A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.592A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.548A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.123A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.807A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.335A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.950A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.103A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.143A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.963A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.942A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.548A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1047 through 1048 removed outlier: 3.966A pdb=" N PHE B1103 " --> pdb=" O VAL B1096 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.582A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.150A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.774A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.264A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.889A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.570A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.998A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AD9, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.410A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.410A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.610A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 897 hydrogen bonds defined for protein. 2496 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: 5.06 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6773 1.35 - 1.47: 5349 1.47 - 1.59: 9675 1.59 - 1.71: 0 1.71 - 1.83: 117 Bond restraints: 21914 Sorted by residual: bond pdb=" C THR B 630 " pdb=" N PRO B 631 " ideal model delta sigma weight residual 1.335 1.378 -0.043 8.70e-03 1.32e+04 2.46e+01 bond pdb=" N GLN B1106 " pdb=" CA GLN B1106 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL B1094 " pdb=" CA VAL B1094 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.38e+00 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.46e+00 ... (remaining 21909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29215 2.44 - 4.89: 517 4.89 - 7.33: 44 7.33 - 9.77: 11 9.77 - 12.21: 3 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C ILE B 834 " pdb=" N LYS B 835 " pdb=" CA LYS B 835 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.08 128.65 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 115.79 110.48 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ASN B1098 " pdb=" CA ASN B1098 " pdb=" C ASN B1098 " ideal model delta sigma weight residual 112.92 107.58 5.34 1.23e+00 6.61e-01 1.89e+01 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12464 17.93 - 35.85: 912 35.85 - 53.78: 155 53.78 - 71.70: 43 71.70 - 89.63: 24 Dihedral angle restraints: 13598 sinusoidal: 5811 harmonic: 7787 Sorted by residual: dihedral pdb=" CA CYS A1082 " pdb=" C CYS A1082 " pdb=" N HIS A1083 " pdb=" CA HIS A1083 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA ASP B 985 " pdb=" C ASP B 985 " pdb=" N LYS B 986 " pdb=" CA LYS B 986 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3501 0.143 - 0.285: 39 0.285 - 0.428: 6 0.428 - 0.571: 1 0.571 - 0.714: 1 Chirality restraints: 3548 Sorted by residual: chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C2 NAG B1208 " pdb=" C1 NAG B1208 " pdb=" C3 NAG B1208 " pdb=" N2 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 3545 not shown) Planarity restraints: 3806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1098 " -0.027 2.00e-02 2.50e+03 2.86e-02 1.02e+01 pdb=" CG ASN B1098 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B1098 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B1098 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1206 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 633 " -0.018 2.00e-02 2.50e+03 1.98e-02 9.78e+00 pdb=" CG TRP A 633 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 633 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 633 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 633 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 633 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 633 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 633 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 633 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 633 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 295 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.036 5.00e-02 4.00e+02 ... (remaining 3803 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5194 2.80 - 3.32: 18596 3.32 - 3.85: 36361 3.85 - 4.37: 41084 4.37 - 4.90: 71700 Nonbonded interactions: 172935 Sorted by model distance: nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.270 3.040 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.299 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.301 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.309 3.040 ... (remaining 172930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 27 through 137 or resid 166 through 210 or resid 216 throu \ gh 623 or resid 638 through 677 or resid 689 through 827 or resid 854 through 12 \ 08)) selection = (chain 'C' and (resid 27 through 331 or resid 528 through 677 or resid 689 throu \ gh 1208)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.040 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21986 Z= 0.225 Angle : 0.820 20.063 29974 Z= 0.421 Chirality : 0.056 0.714 3548 Planarity : 0.006 0.065 3775 Dihedral : 13.344 89.626 8472 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % 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: -1.30 (0.15), residues: 2622 helix: -0.79 (0.17), residues: 632 sheet: 0.05 (0.24), residues: 468 loop : -1.19 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.021 0.002 TYR A 904 PHE 0.040 0.002 PHE A 275 TRP 0.052 0.002 TRP A 633 HIS 0.010 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00434 (21914) covalent geometry : angle 0.76143 (29790) SS BOND : bond 0.00440 ( 32) SS BOND : angle 1.58699 ( 64) hydrogen bonds : bond 0.20363 ( 891) hydrogen bonds : angle 9.04856 ( 2496) link_BETA1-4 : bond 0.01737 ( 9) link_BETA1-4 : angle 6.36256 ( 27) link_NAG-ASN : bond 0.00818 ( 31) link_NAG-ASN : angle 4.17733 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7392 (m-90) cc_final: 0.6960 (m-90) REVERT: B 740 MET cc_start: 0.8440 (tpp) cc_final: 0.8163 (tpt) REVERT: C 1029 MET cc_start: 0.7708 (tpp) cc_final: 0.7497 (tpp) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.1575 time to fit residues: 15.6333 Evaluate side-chains 45 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 901 GLN B 913 GLN B 919 ASN B1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.073030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.057801 restraints weight = 127881.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.058206 restraints weight = 76153.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.058662 restraints weight = 57187.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.058732 restraints weight = 53507.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.058818 restraints weight = 46679.088| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21986 Z= 0.258 Angle : 0.714 14.008 29974 Z= 0.363 Chirality : 0.048 0.599 3548 Planarity : 0.005 0.077 3775 Dihedral : 7.500 56.883 3679 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 2622 helix: 0.33 (0.20), residues: 629 sheet: -0.43 (0.21), residues: 562 loop : -1.08 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 319 TYR 0.027 0.002 TYR C1067 PHE 0.024 0.002 PHE B1089 TRP 0.035 0.002 TRP A 633 HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00565 (21914) covalent geometry : angle 0.68753 (29790) SS BOND : bond 0.00456 ( 32) SS BOND : angle 0.89119 ( 64) hydrogen bonds : bond 0.04769 ( 891) hydrogen bonds : angle 6.81536 ( 2496) link_BETA1-4 : bond 0.00651 ( 9) link_BETA1-4 : angle 4.04596 ( 27) link_NAG-ASN : bond 0.00482 ( 31) link_NAG-ASN : angle 2.76869 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7174 (m-90) cc_final: 0.6582 (m-90) REVERT: A 1050 MET cc_start: 0.6935 (mtt) cc_final: 0.6654 (mtt) REVERT: B 740 MET cc_start: 0.8996 (tpp) cc_final: 0.8425 (tpt) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.1335 time to fit residues: 11.9479 Evaluate side-chains 45 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 185 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 580 GLN B 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.072854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.057914 restraints weight = 128184.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.058084 restraints weight = 87997.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058244 restraints weight = 64121.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.058429 restraints weight = 58468.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058495 restraints weight = 53010.981| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21986 Z= 0.199 Angle : 0.633 14.390 29974 Z= 0.318 Chirality : 0.047 0.553 3548 Planarity : 0.004 0.055 3775 Dihedral : 7.164 57.887 3679 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.73 % Allowed : 7.13 % Favored : 92.14 % 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: -0.85 (0.16), residues: 2622 helix: 0.79 (0.20), residues: 632 sheet: -0.66 (0.22), residues: 516 loop : -1.13 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.024 0.002 TYR C 170 PHE 0.023 0.002 PHE B 318 TRP 0.026 0.002 TRP A 633 HIS 0.006 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00435 (21914) covalent geometry : angle 0.60330 (29790) SS BOND : bond 0.00366 ( 32) SS BOND : angle 0.86111 ( 64) hydrogen bonds : bond 0.04311 ( 891) hydrogen bonds : angle 6.29315 ( 2496) link_BETA1-4 : bond 0.01028 ( 9) link_BETA1-4 : angle 4.06209 ( 27) link_NAG-ASN : bond 0.00490 ( 31) link_NAG-ASN : angle 2.68239 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.768 Fit side-chains REVERT: A 633 TRP cc_start: 0.7430 (m-90) cc_final: 0.7096 (m-10) REVERT: A 1050 MET cc_start: 0.6777 (mtt) cc_final: 0.6542 (mtt) REVERT: B 740 MET cc_start: 0.9073 (tpp) cc_final: 0.8788 (tpp) outliers start: 17 outliers final: 7 residues processed: 58 average time/residue: 0.1313 time to fit residues: 13.1375 Evaluate side-chains 45 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.071996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.057355 restraints weight = 128761.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056933 restraints weight = 93987.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.057288 restraints weight = 71297.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057568 restraints weight = 61464.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057591 restraints weight = 55544.230| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21986 Z= 0.260 Angle : 0.702 13.145 29974 Z= 0.353 Chirality : 0.048 0.565 3548 Planarity : 0.005 0.062 3775 Dihedral : 7.371 58.279 3679 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.28 % Allowed : 9.78 % Favored : 88.94 % 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: -1.09 (0.16), residues: 2622 helix: 0.51 (0.20), residues: 638 sheet: -0.91 (0.22), residues: 509 loop : -1.22 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 319 TYR 0.030 0.002 TYR C1067 PHE 0.020 0.002 PHE B1089 TRP 0.021 0.002 TRP A 633 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00573 (21914) covalent geometry : angle 0.67431 (29790) SS BOND : bond 0.00509 ( 32) SS BOND : angle 1.05346 ( 64) hydrogen bonds : bond 0.04502 ( 891) hydrogen bonds : angle 6.41875 ( 2496) link_BETA1-4 : bond 0.00788 ( 9) link_BETA1-4 : angle 3.93206 ( 27) link_NAG-ASN : bond 0.00572 ( 31) link_NAG-ASN : angle 2.79778 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.783 Fit side-chains REVERT: B 233 ILE cc_start: 0.8051 (mt) cc_final: 0.7694 (mm) REVERT: B 740 MET cc_start: 0.9071 (tpp) cc_final: 0.8762 (tpp) outliers start: 30 outliers final: 19 residues processed: 71 average time/residue: 0.1180 time to fit residues: 15.1013 Evaluate side-chains 56 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 32 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 210 optimal weight: 0.0040 chunk 192 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.073326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058533 restraints weight = 127419.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.058768 restraints weight = 84188.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.059082 restraints weight = 61271.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.059298 restraints weight = 56135.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059340 restraints weight = 49385.242| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21986 Z= 0.114 Angle : 0.556 13.899 29974 Z= 0.278 Chirality : 0.045 0.535 3548 Planarity : 0.004 0.050 3775 Dihedral : 6.862 57.735 3679 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.77 % Allowed : 10.59 % Favored : 88.64 % 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: -0.65 (0.16), residues: 2622 helix: 1.19 (0.21), residues: 637 sheet: -0.57 (0.21), residues: 568 loop : -1.14 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.016 0.001 TYR A 904 PHE 0.019 0.001 PHE B 318 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00241 (21914) covalent geometry : angle 0.52705 (29790) SS BOND : bond 0.00211 ( 32) SS BOND : angle 0.74187 ( 64) hydrogen bonds : bond 0.03619 ( 891) hydrogen bonds : angle 5.83443 ( 2496) link_BETA1-4 : bond 0.00983 ( 9) link_BETA1-4 : angle 3.76292 ( 27) link_NAG-ASN : bond 0.00425 ( 31) link_NAG-ASN : angle 2.45196 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.831 Fit side-chains REVERT: A 374 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6209 (p90) REVERT: A 900 MET cc_start: 0.5685 (pmm) cc_final: 0.4742 (pmm) REVERT: A 1050 MET cc_start: 0.6614 (mtt) cc_final: 0.6381 (mtt) REVERT: B 740 MET cc_start: 0.9081 (tpp) cc_final: 0.8798 (tpp) outliers start: 18 outliers final: 7 residues processed: 57 average time/residue: 0.1318 time to fit residues: 13.4113 Evaluate side-chains 44 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 262 optimal weight: 0.0870 chunk 14 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 overall best weight: 2.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A1054 GLN B 137 ASN ** B 913 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.072871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.058002 restraints weight = 127511.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.058176 restraints weight = 89150.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.058245 restraints weight = 65128.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058539 restraints weight = 59742.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.058552 restraints weight = 53671.833| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21986 Z= 0.153 Angle : 0.579 10.612 29974 Z= 0.288 Chirality : 0.045 0.428 3548 Planarity : 0.004 0.047 3775 Dihedral : 7.075 79.711 3679 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.24 % Allowed : 10.63 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2622 helix: 1.32 (0.21), residues: 629 sheet: -0.70 (0.22), residues: 528 loop : -1.06 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.023 0.001 TYR C1067 PHE 0.016 0.001 PHE B 318 TRP 0.012 0.001 TRP A1102 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (21914) covalent geometry : angle 0.55237 (29790) SS BOND : bond 0.00328 ( 32) SS BOND : angle 0.73263 ( 64) hydrogen bonds : bond 0.03708 ( 891) hydrogen bonds : angle 5.81709 ( 2496) link_BETA1-4 : bond 0.00894 ( 9) link_BETA1-4 : angle 3.73003 ( 27) link_NAG-ASN : bond 0.00358 ( 31) link_NAG-ASN : angle 2.42047 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.768 Fit side-chains REVERT: A 374 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6161 (p90) REVERT: B 740 MET cc_start: 0.9085 (tpp) cc_final: 0.8795 (tpp) outliers start: 29 outliers final: 18 residues processed: 67 average time/residue: 0.1292 time to fit residues: 15.0134 Evaluate side-chains 56 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 139 optimal weight: 0.0870 chunk 204 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 overall best weight: 4.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.072137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.057429 restraints weight = 128401.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.057399 restraints weight = 95918.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.057587 restraints weight = 69707.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.057784 restraints weight = 61999.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.057869 restraints weight = 56428.259| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21986 Z= 0.218 Angle : 0.639 11.024 29974 Z= 0.319 Chirality : 0.046 0.324 3548 Planarity : 0.004 0.051 3775 Dihedral : 7.280 84.363 3679 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.58 % Allowed : 11.27 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2622 helix: 1.00 (0.21), residues: 635 sheet: -0.98 (0.21), residues: 534 loop : -1.07 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 905 TYR 0.049 0.002 TYR A 449 PHE 0.020 0.002 PHE B1089 TRP 0.014 0.001 TRP A1102 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00482 (21914) covalent geometry : angle 0.61417 (29790) SS BOND : bond 0.00434 ( 32) SS BOND : angle 0.82520 ( 64) hydrogen bonds : bond 0.04040 ( 891) hydrogen bonds : angle 6.01148 ( 2496) link_BETA1-4 : bond 0.00860 ( 9) link_BETA1-4 : angle 3.78997 ( 27) link_NAG-ASN : bond 0.00430 ( 31) link_NAG-ASN : angle 2.49964 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 42 time to evaluate : 0.729 Fit side-chains REVERT: A 374 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6095 (p90) REVERT: A 1050 MET cc_start: 0.6835 (mtt) cc_final: 0.6455 (mtt) REVERT: B 740 MET cc_start: 0.9050 (tpp) cc_final: 0.8749 (tpp) REVERT: C 92 PHE cc_start: 0.4961 (t80) cc_final: 0.4713 (t80) outliers start: 37 outliers final: 29 residues processed: 76 average time/residue: 0.1345 time to fit residues: 17.6805 Evaluate side-chains 68 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 38 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 148 optimal weight: 8.9990 chunk 245 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 203 optimal weight: 40.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 804 GLN B1071 GLN C 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.073411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.058694 restraints weight = 129446.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.058994 restraints weight = 86720.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.059119 restraints weight = 63226.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.059302 restraints weight = 60074.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059412 restraints weight = 51402.725| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21986 Z= 0.108 Angle : 0.543 10.704 29974 Z= 0.271 Chirality : 0.044 0.295 3548 Planarity : 0.004 0.050 3775 Dihedral : 6.882 79.544 3679 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.02 % Allowed : 11.83 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2622 helix: 1.46 (0.21), residues: 635 sheet: -0.57 (0.22), residues: 558 loop : -1.02 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE B 318 TRP 0.009 0.001 TRP A 104 HIS 0.007 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00228 (21914) covalent geometry : angle 0.51922 (29790) SS BOND : bond 0.00204 ( 32) SS BOND : angle 0.65318 ( 64) hydrogen bonds : bond 0.03446 ( 891) hydrogen bonds : angle 5.57815 ( 2496) link_BETA1-4 : bond 0.01023 ( 9) link_BETA1-4 : angle 3.65531 ( 27) link_NAG-ASN : bond 0.00231 ( 31) link_NAG-ASN : angle 2.14250 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.755 Fit side-chains REVERT: A 374 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5984 (p90) REVERT: B 740 MET cc_start: 0.9057 (tpp) cc_final: 0.8782 (tpp) REVERT: B 964 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8140 (mtmm) outliers start: 24 outliers final: 17 residues processed: 63 average time/residue: 0.1359 time to fit residues: 14.7424 Evaluate side-chains 56 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 133 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 0.0770 chunk 174 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.073225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.058491 restraints weight = 130007.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.058865 restraints weight = 85984.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059085 restraints weight = 65145.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.059321 restraints weight = 57841.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.059342 restraints weight = 50118.771| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21986 Z= 0.122 Angle : 0.547 10.467 29974 Z= 0.271 Chirality : 0.044 0.275 3548 Planarity : 0.004 0.046 3775 Dihedral : 6.762 77.398 3679 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.85 % Allowed : 12.17 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2622 helix: 1.52 (0.21), residues: 636 sheet: -0.69 (0.22), residues: 506 loop : -0.96 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.041 0.001 TYR A 449 PHE 0.014 0.001 PHE B 135 TRP 0.009 0.001 TRP A1102 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00265 (21914) covalent geometry : angle 0.52355 (29790) SS BOND : bond 0.00247 ( 32) SS BOND : angle 0.64255 ( 64) hydrogen bonds : bond 0.03479 ( 891) hydrogen bonds : angle 5.52700 ( 2496) link_BETA1-4 : bond 0.00980 ( 9) link_BETA1-4 : angle 3.63870 ( 27) link_NAG-ASN : bond 0.00225 ( 31) link_NAG-ASN : angle 2.10220 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.723 Fit side-chains REVERT: A 374 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5970 (p90) REVERT: B 740 MET cc_start: 0.9061 (tpp) cc_final: 0.8765 (tpp) REVERT: B 964 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8047 (mtmm) outliers start: 20 outliers final: 18 residues processed: 55 average time/residue: 0.1221 time to fit residues: 12.0479 Evaluate side-chains 56 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 263 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 57 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 177 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.073975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059244 restraints weight = 130188.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.059607 restraints weight = 85237.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.059815 restraints weight = 64041.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.059909 restraints weight = 58459.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.060030 restraints weight = 51746.981| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21986 Z= 0.093 Angle : 0.517 10.307 29974 Z= 0.257 Chirality : 0.043 0.256 3548 Planarity : 0.003 0.045 3775 Dihedral : 6.449 72.958 3679 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.98 % Allowed : 12.00 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2622 helix: 1.86 (0.21), residues: 627 sheet: -0.49 (0.21), residues: 563 loop : -0.90 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.015 0.001 TYR B1067 PHE 0.017 0.001 PHE C 92 TRP 0.011 0.001 TRP C1102 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00197 (21914) covalent geometry : angle 0.49542 (29790) SS BOND : bond 0.00156 ( 32) SS BOND : angle 0.60576 ( 64) hydrogen bonds : bond 0.03224 ( 891) hydrogen bonds : angle 5.26091 ( 2496) link_BETA1-4 : bond 0.01073 ( 9) link_BETA1-4 : angle 3.56546 ( 27) link_NAG-ASN : bond 0.00212 ( 31) link_NAG-ASN : angle 1.90225 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.780 Fit side-chains REVERT: A 374 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5956 (p90) REVERT: A 900 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.4770 (pmm) REVERT: B 740 MET cc_start: 0.9071 (tpp) cc_final: 0.8757 (tpp) REVERT: B 964 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8100 (mtmm) REVERT: B 986 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.6683 (tptp) outliers start: 23 outliers final: 19 residues processed: 66 average time/residue: 0.1288 time to fit residues: 14.9507 Evaluate side-chains 62 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.073898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059234 restraints weight = 130831.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059491 restraints weight = 85495.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.059796 restraints weight = 64862.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.059908 restraints weight = 57856.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.059991 restraints weight = 52597.958| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.617 21986 Z= 0.232 Angle : 0.749 59.197 29974 Z= 0.411 Chirality : 0.044 0.358 3548 Planarity : 0.003 0.045 3775 Dihedral : 6.464 72.944 3679 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.94 % Allowed : 12.08 % Favored : 86.98 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2622 helix: 1.86 (0.21), residues: 627 sheet: -0.47 (0.21), residues: 563 loop : -0.90 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.015 0.001 TYR B1067 PHE 0.017 0.001 PHE C 92 TRP 0.010 0.001 TRP C1102 HIS 0.004 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00602 (21914) covalent geometry : angle 0.69133 (29790) SS BOND : bond 0.01589 ( 32) SS BOND : angle 5.45897 ( 64) hydrogen bonds : bond 0.03247 ( 891) hydrogen bonds : angle 5.25936 ( 2496) link_BETA1-4 : bond 0.01031 ( 9) link_BETA1-4 : angle 3.57192 ( 27) link_NAG-ASN : bond 0.00208 ( 31) link_NAG-ASN : angle 1.90260 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.04 seconds wall clock time: 49 minutes 37.55 seconds (2977.55 seconds total)