Starting phenix.real_space_refine on Sat Jul 4 15:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tge_25880/07_2026/7tge_25880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tge_25880/07_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_25880/07_2026/7tge_25880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tge_25880/07_2026/7tge_25880.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tge_25880/07_2026/7tge_25880.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tge_25880/07_2026/7tge_25880.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tge_25880/07_2026/7tge_25880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tge_25880/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 4.18, per 1000 atoms: 0.19 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: 1.71 Conformation dependent library (CDL) restraints added in 983.4 milliseconds 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: 0.57 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: 4.44 Time building geometry restraints manager: 2.32 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: 11706 17.93 - 35.85: 867 35.85 - 53.78: 131 53.78 - 71.70: 30 71.70 - 89.63: 24 Dihedral angle restraints: 12758 sinusoidal: 4971 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 12755 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: 1.730 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.800 Find NCS groups from input model: 0.420 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 13.389 89.626 7632 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/Z covalent geometry : bond 0.00434 / 0.22 (21914) covalent geometry : angle 0.76143 / 0.41 (29790) SS BOND : bond 0.00440 / 0.32 ( 32) SS BOND : angle 1.58699 / 1.20 ( 64) hydrogen bonds : bond 0.20363 / 13.09 ( 891) hydrogen bonds : angle 9.04856 / 6.26 ( 2496) link_BETA1-4 : bond 0.01737 / 1.16 ( 9) link_BETA1-4 : angle 6.36256 / 3.60 ( 27) link_NAG-ASN : bond 0.00818 / 0.55 ( 31) link_NAG-ASN : angle 4.17733 / 3.24 ( 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 : 0.703 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: 0.1398 time to fit residues: 14.0052 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 : 0.765 ------------------------------------------------------------------------------- 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... 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 = 0.3984 r_free = 0.3984 target = 0.072998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058260 restraints weight = 127926.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058362 restraints weight = 77839.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058565 restraints weight = 59958.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.058742 restraints weight = 54897.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.058805 restraints weight = 49137.711| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21986 Z= 0.259 Angle : 0.714 13.745 29974 Z= 0.362 Chirality : 0.048 0.576 3548 Planarity : 0.005 0.067 3775 Dihedral : 5.408 26.301 2839 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2622 helix: 0.32 (0.20), residues: 632 sheet: -0.47 (0.21), residues: 562 loop : -1.08 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 319 TYR 0.027 0.002 TYR C1067 PHE 0.026 0.002 PHE B1089 TRP 0.035 0.002 TRP A 633 HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (21914) covalent geometry : angle 0.68953 / 0.36 (29790) SS BOND : bond 0.00465 / 0.33 ( 32) SS BOND : angle 0.95131 / 0.72 ( 64) hydrogen bonds : bond 0.04655 / 3.07 ( 891) hydrogen bonds : angle 6.79984 / 4.70 ( 2496) link_BETA1-4 : bond 0.00617 / 0.45 ( 9) link_BETA1-4 : angle 3.63900 / 2.03 ( 27) link_NAG-ASN : bond 0.00514 / 0.36 ( 31) link_NAG-ASN : angle 2.72717 / 1.91 ( 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 : 0.729 Fit side-chains revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7209 (m-90) cc_final: 0.6598 (m-90) REVERT: A 1050 MET cc_start: 0.6948 (mtt) cc_final: 0.6666 (mtt) REVERT: B 740 MET cc_start: 0.8980 (tpp) cc_final: 0.8409 (tpt) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.1266 time to fit residues: 11.3825 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 : 0.694 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.073990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.058935 restraints weight = 127727.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.059377 restraints weight = 79116.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059519 restraints weight = 57318.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.059742 restraints weight = 56065.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059791 restraints weight = 48838.296| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21986 Z= 0.123 Angle : 0.561 14.723 29974 Z= 0.281 Chirality : 0.045 0.532 3548 Planarity : 0.004 0.047 3775 Dihedral : 4.899 24.238 2839 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.85 % 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: -0.57 (0.16), residues: 2622 helix: 1.11 (0.21), residues: 626 sheet: -0.34 (0.21), residues: 552 loop : -1.06 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.029 0.001 TYR A 904 PHE 0.022 0.001 PHE B 318 TRP 0.021 0.001 TRP A 633 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (21914) covalent geometry : angle 0.53442 / 0.28 (29790) SS BOND : bond 0.00253 / 0.18 ( 32) SS BOND : angle 0.71069 / 0.55 ( 64) hydrogen bonds : bond 0.03889 / 2.61 ( 891) hydrogen bonds : angle 6.11011 / 4.25 ( 2496) link_BETA1-4 : bond 0.00961 / 0.69 ( 9) link_BETA1-4 : angle 3.42547 / 1.91 ( 27) link_NAG-ASN : bond 0.00448 / 0.30 ( 31) link_NAG-ASN : angle 2.51763 / 1.79 ( 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 55 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.797 Fit side-chains REVERT: A 1050 MET cc_start: 0.6599 (mtt) cc_final: 0.6306 (mtm) REVERT: B 740 MET cc_start: 0.9040 (tpp) cc_final: 0.8749 (tpp) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.1286 time to fit residues: 12.2368 Evaluate side-chains 44 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 902 MET Chi-restraints excluded: chain B residue 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 172 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.072437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.057789 restraints weight = 128278.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057510 restraints weight = 83979.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.057677 restraints weight = 68527.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.057831 restraints weight = 64150.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.057935 restraints weight = 54654.563| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21986 Z= 0.233 Angle : 0.665 13.091 29974 Z= 0.334 Chirality : 0.047 0.533 3548 Planarity : 0.004 0.057 3775 Dihedral : 5.157 25.246 2839 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.94 % Allowed : 8.11 % Favored : 90.95 % 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: -0.84 (0.16), residues: 2622 helix: 0.77 (0.20), residues: 633 sheet: -0.65 (0.21), residues: 540 loop : -1.12 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 905 TYR 0.027 0.002 TYR C1067 PHE 0.021 0.002 PHE B1089 TRP 0.016 0.002 TRP A1102 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (21914) covalent geometry : angle 0.64160 / 0.33 (29790) SS BOND : bond 0.00439 / 0.33 ( 32) SS BOND : angle 0.87318 / 0.66 ( 64) hydrogen bonds : bond 0.04334 / 2.87 ( 891) hydrogen bonds : angle 6.26184 / 4.34 ( 2496) link_BETA1-4 : bond 0.00860 / 0.63 ( 9) link_BETA1-4 : angle 3.22739 / 1.82 ( 27) link_NAG-ASN : bond 0.00522 / 0.35 ( 31) link_NAG-ASN : angle 2.63861 / 1.83 ( 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 66 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.637 Fit side-chains REVERT: A 633 TRP cc_start: 0.6687 (m-10) cc_final: 0.6414 (m-10) REVERT: B 233 ILE cc_start: 0.8059 (mt) cc_final: 0.7719 (mm) REVERT: B 740 MET cc_start: 0.9080 (tpp) cc_final: 0.8769 (tpp) outliers start: 22 outliers final: 14 residues processed: 64 average time/residue: 0.1270 time to fit residues: 14.1302 Evaluate side-chains 50 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 912 THR 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 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 770 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 32 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 233 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.072277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.057750 restraints weight = 128378.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.057473 restraints weight = 89463.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.057622 restraints weight = 72009.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.057772 restraints weight = 66965.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.057935 restraints weight = 57861.129| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21986 Z= 0.223 Angle : 0.650 13.148 29974 Z= 0.326 Chirality : 0.046 0.519 3548 Planarity : 0.004 0.057 3775 Dihedral : 5.158 24.750 2839 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.45 % Allowed : 9.56 % Favored : 88.98 % 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: -0.94 (0.16), residues: 2622 helix: 0.79 (0.20), residues: 636 sheet: -0.84 (0.21), residues: 525 loop : -1.18 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.025 0.002 TYR C1067 PHE 0.018 0.002 PHE B1089 TRP 0.014 0.002 TRP A1102 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (21914) covalent geometry : angle 0.62724 / 0.32 (29790) SS BOND : bond 0.00416 / 0.31 ( 32) SS BOND : angle 1.06681 / 0.72 ( 64) hydrogen bonds : bond 0.04152 / 2.77 ( 891) hydrogen bonds : angle 6.17416 / 4.28 ( 2496) link_BETA1-4 : bond 0.00791 / 0.55 ( 9) link_BETA1-4 : angle 3.00046 / 1.74 ( 27) link_NAG-ASN : bond 0.00477 / 0.32 ( 31) link_NAG-ASN : angle 2.60319 / 1.82 ( 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 76 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 42 time to evaluate : 0.822 Fit side-chains REVERT: A 374 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6221 (p90) REVERT: A 633 TRP cc_start: 0.6727 (m-10) cc_final: 0.6363 (m-90) REVERT: A 900 MET cc_start: 0.5750 (pmm) cc_final: 0.4822 (pmm) REVERT: B 740 MET cc_start: 0.9062 (tpp) cc_final: 0.8757 (tpp) outliers start: 34 outliers final: 19 residues processed: 73 average time/residue: 0.1124 time to fit residues: 14.6636 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 : 0.837 ------------------------------------------------------------------------------- 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 734 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 299 THR 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 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 1009 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 chunk 224 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 262 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 GLN B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.073200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.058624 restraints weight = 127138.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.058786 restraints weight = 82472.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059041 restraints weight = 62687.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.059181 restraints weight = 55131.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.059259 restraints weight = 50724.868| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21986 Z= 0.123 Angle : 0.566 11.246 29974 Z= 0.282 Chirality : 0.044 0.307 3548 Planarity : 0.004 0.052 3775 Dihedral : 4.795 22.676 2839 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.07 % Allowed : 10.25 % Favored : 88.68 % 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: -0.60 (0.16), residues: 2622 helix: 1.33 (0.21), residues: 629 sheet: -0.67 (0.21), residues: 552 loop : -1.08 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE B 906 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21914) covalent geometry : angle 0.54588 / 0.28 (29790) SS BOND : bond 0.00234 / 0.16 ( 32) SS BOND : angle 0.75536 / 0.53 ( 64) hydrogen bonds : bond 0.03609 / 2.43 ( 891) hydrogen bonds : angle 5.78966 / 4.02 ( 2496) link_BETA1-4 : bond 0.00995 / 0.73 ( 9) link_BETA1-4 : angle 2.81039 / 1.61 ( 27) link_NAG-ASN : bond 0.00305 / 0.20 ( 31) link_NAG-ASN : angle 2.26036 / 1.58 ( 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 67 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.692 Fit side-chains REVERT: A 374 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.6106 (p90) REVERT: A 633 TRP cc_start: 0.6634 (m-10) cc_final: 0.6268 (m-90) REVERT: A 900 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.4861 (pmm) REVERT: B 740 MET cc_start: 0.9046 (tpp) cc_final: 0.8773 (tpp) REVERT: C 987 VAL cc_start: 0.8889 (m) cc_final: 0.8681 (p) outliers start: 25 outliers final: 13 residues processed: 64 average time/residue: 0.1269 time to fit residues: 14.2086 Evaluate side-chains 52 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 913 GLN Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1009 THR 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: 0.0970 chunk 204 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.072569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.057747 restraints weight = 127725.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.057907 restraints weight = 89088.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.057962 restraints weight = 66156.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058139 restraints weight = 64181.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.058285 restraints weight = 54429.845| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21986 Z= 0.177 Angle : 0.594 10.958 29974 Z= 0.296 Chirality : 0.045 0.312 3548 Planarity : 0.004 0.050 3775 Dihedral : 4.840 23.377 2839 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.24 % Allowed : 10.20 % Favored : 88.56 % 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: -0.68 (0.16), residues: 2622 helix: 1.17 (0.21), residues: 635 sheet: -0.84 (0.22), residues: 524 loop : -1.03 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.038 0.002 TYR A 449 PHE 0.016 0.001 PHE B1089 TRP 0.013 0.001 TRP A1102 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (21914) covalent geometry : angle 0.57475 / 0.29 (29790) SS BOND : bond 0.00346 / 0.26 ( 32) SS BOND : angle 0.75051 / 0.54 ( 64) hydrogen bonds : bond 0.03813 / 2.55 ( 891) hydrogen bonds : angle 5.84324 / 4.06 ( 2496) link_BETA1-4 : bond 0.00853 / 0.62 ( 9) link_BETA1-4 : angle 2.69588 / 1.58 ( 27) link_NAG-ASN : bond 0.00329 / 0.21 ( 31) link_NAG-ASN : angle 2.29869 / 1.58 ( 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 70 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.774 Fit side-chains REVERT: A 374 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 633 TRP cc_start: 0.6669 (m-10) cc_final: 0.6281 (m-90) REVERT: A 1050 MET cc_start: 0.6849 (mtt) cc_final: 0.6575 (mtt) REVERT: B 740 MET cc_start: 0.9037 (tpp) cc_final: 0.8747 (tpp) outliers start: 29 outliers final: 23 residues processed: 67 average time/residue: 0.1157 time to fit residues: 13.4645 Evaluate side-chains 63 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 986 LYS 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 1106 GLN Chi-restraints excluded: chain C residue 312 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 148 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 203 optimal weight: 50.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.073145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.058499 restraints weight = 127929.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.058695 restraints weight = 78795.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058970 restraints weight = 57218.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.059131 restraints weight = 53610.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059166 restraints weight = 48028.473| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2566 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= 0.123 Angle : 0.550 11.142 29974 Z= 0.274 Chirality : 0.044 0.259 3548 Planarity : 0.004 0.050 3775 Dihedral : 4.689 22.377 2839 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.02 % Allowed : 10.67 % Favored : 88.30 % 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: -0.53 (0.16), residues: 2622 helix: 1.38 (0.21), residues: 635 sheet: -0.61 (0.22), residues: 529 loop : -1.04 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 498 TYR 0.022 0.001 TYR A 501 PHE 0.012 0.001 PHE C 92 TRP 0.010 0.001 TRP A1102 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21914) covalent geometry : angle 0.53208 / 0.27 (29790) SS BOND : bond 0.00259 / 0.17 ( 32) SS BOND : angle 0.67891 / 0.49 ( 64) hydrogen bonds : bond 0.03553 / 2.38 ( 891) hydrogen bonds : angle 5.64950 / 3.93 ( 2496) link_BETA1-4 : bond 0.00917 / 0.66 ( 9) link_BETA1-4 : angle 2.59446 / 1.53 ( 27) link_NAG-ASN : bond 0.00235 / 0.14 ( 31) link_NAG-ASN : angle 2.09814 / 1.45 ( 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 63 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.856 Fit side-chains REVERT: A 374 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.6007 (p90) REVERT: A 633 TRP cc_start: 0.6592 (m-10) cc_final: 0.6191 (m-90) REVERT: B 740 MET cc_start: 0.9061 (tpp) cc_final: 0.8781 (tpp) outliers start: 24 outliers final: 20 residues processed: 60 average time/residue: 0.1372 time to fit residues: 14.4714 Evaluate side-chains 57 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 913 GLN Chi-restraints excluded: chain B residue 986 LYS 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 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 133 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.073026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.057903 restraints weight = 128111.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.058304 restraints weight = 85647.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058483 restraints weight = 62323.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.058764 restraints weight = 56723.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.058804 restraints weight = 50725.511| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21986 Z= 0.131 Angle : 0.550 11.176 29974 Z= 0.274 Chirality : 0.044 0.256 3548 Planarity : 0.004 0.048 3775 Dihedral : 4.621 22.360 2839 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.07 % Allowed : 10.89 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2622 helix: 1.42 (0.21), residues: 635 sheet: -0.60 (0.22), residues: 527 loop : -1.00 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.025 0.001 TYR A 449 PHE 0.012 0.001 PHE C 92 TRP 0.009 0.001 TRP A 633 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21914) covalent geometry : angle 0.53334 / 0.27 (29790) SS BOND : bond 0.00268 / 0.19 ( 32) SS BOND : angle 0.66197 / 0.48 ( 64) hydrogen bonds : bond 0.03535 / 2.37 ( 891) hydrogen bonds : angle 5.59515 / 3.89 ( 2496) link_BETA1-4 : bond 0.00925 / 0.67 ( 9) link_BETA1-4 : angle 2.51110 / 1.49 ( 27) link_NAG-ASN : bond 0.00215 / 0.13 ( 31) link_NAG-ASN : angle 2.02034 / 1.39 ( 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 63 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 0.811 Fit side-chains REVERT: A 374 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.6026 (p90) REVERT: A 633 TRP cc_start: 0.6628 (m-10) cc_final: 0.6214 (m-10) REVERT: A 1050 MET cc_start: 0.6807 (mtt) cc_final: 0.6452 (mtt) REVERT: B 740 MET cc_start: 0.9072 (tpp) cc_final: 0.8785 (tpp) outliers start: 25 outliers final: 21 residues processed: 60 average time/residue: 0.1315 time to fit residues: 14.1376 Evaluate side-chains 59 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 A residue 1104 VAL 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 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 1009 THR Chi-restraints excluded: chain B residue 1033 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 263 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.073521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.058570 restraints weight = 130087.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058983 restraints weight = 87481.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.059193 restraints weight = 64222.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059459 restraints weight = 56623.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059486 restraints weight = 50647.081| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21986 Z= 0.111 Angle : 0.523 11.125 29974 Z= 0.261 Chirality : 0.043 0.254 3548 Planarity : 0.003 0.047 3775 Dihedral : 4.424 21.474 2839 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.94 % Allowed : 11.19 % Favored : 87.87 % 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: -0.34 (0.16), residues: 2622 helix: 1.58 (0.21), residues: 637 sheet: -0.53 (0.21), residues: 559 loop : -0.93 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.019 0.001 TYR C1067 PHE 0.012 0.001 PHE C 92 TRP 0.010 0.001 TRP A 633 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (21914) covalent geometry : angle 0.50930 / 0.26 (29790) SS BOND : bond 0.00207 / 0.14 ( 32) SS BOND : angle 0.62745 / 0.45 ( 64) hydrogen bonds : bond 0.03375 / 2.26 ( 891) hydrogen bonds : angle 5.39747 / 3.75 ( 2496) link_BETA1-4 : bond 0.01010 / 0.74 ( 9) link_BETA1-4 : angle 2.34472 / 1.43 ( 27) link_NAG-ASN : bond 0.00182 / 0.11 ( 31) link_NAG-ASN : angle 1.81187 / 1.25 ( 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 63 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.841 Fit side-chains REVERT: A 374 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.6003 (p90) REVERT: A 633 TRP cc_start: 0.6601 (m-10) cc_final: 0.6206 (m-10) REVERT: A 1029 MET cc_start: 0.8443 (tpp) cc_final: 0.8157 (tpp) REVERT: B 740 MET cc_start: 0.9080 (tpp) cc_final: 0.8796 (tpp) outliers start: 22 outliers final: 18 residues processed: 60 average time/residue: 0.1344 time to fit residues: 14.3701 Evaluate side-chains 57 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1009 THR Chi-restraints excluded: chain B residue 1033 VAL 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 951 VAL 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: 9.9990 chunk 250 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 124 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.073711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.058941 restraints weight = 128408.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.059072 restraints weight = 87091.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.059522 restraints weight = 62181.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.059667 restraints weight = 55635.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.059714 restraints weight = 49709.873| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21986 Z= 0.096 Angle : 0.512 10.562 29974 Z= 0.256 Chirality : 0.043 0.252 3548 Planarity : 0.003 0.047 3775 Dihedral : 4.334 26.088 2839 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.77 % Allowed : 11.27 % Favored : 87.96 % 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: -0.24 (0.17), residues: 2622 helix: 1.71 (0.21), residues: 637 sheet: -0.48 (0.21), residues: 561 loop : -0.89 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.021 0.001 TYR A 449 PHE 0.013 0.001 PHE C 92 TRP 0.010 0.001 TRP A 633 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (21914) covalent geometry : angle 0.49840 / 0.25 (29790) SS BOND : bond 0.00170 / 0.11 ( 32) SS BOND : angle 0.75270 / 0.53 ( 64) hydrogen bonds : bond 0.03261 / 2.19 ( 891) hydrogen bonds : angle 5.28437 / 3.67 ( 2496) link_BETA1-4 : bond 0.01005 / 0.75 ( 9) link_BETA1-4 : angle 2.23543 / 1.37 ( 27) link_NAG-ASN : bond 0.00196 / 0.11 ( 31) link_NAG-ASN : angle 1.71660 / 1.18 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2716.25 seconds wall clock time: 48 minutes 27.09 seconds (2907.09 seconds total)