Starting phenix.real_space_refine on Wed Jun 18 22:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tge_25880/06_2025/7tge_25880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tge_25880/06_2025/7tge_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_25880/06_2025/7tge_25880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tge_25880/06_2025/7tge_25880.map" model { file = "/net/cci-nas-00/data/ceres_data/7tge_25880/06_2025/7tge_25880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tge_25880/06_2025/7tge_25880.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21461 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8076 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6562 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 803} Chain breaks: 8 Chain: "C" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6263 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 767} Chain breaks: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.98, per 1000 atoms: 0.60 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: 5.89 Conformation dependent library (CDL) restraints added in 3.0 seconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 27.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 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: 9.64 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6773 1.35 - 1.47: 5349 1.47 - 1.59: 9675 1.59 - 1.71: 0 1.71 - 1.83: 117 Bond restraints: 21914 Sorted by residual: bond pdb=" C THR B 630 " pdb=" N PRO B 631 " ideal model delta sigma weight residual 1.335 1.378 -0.043 8.70e-03 1.32e+04 2.46e+01 bond pdb=" N GLN B1106 " pdb=" CA GLN B1106 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL B1094 " pdb=" CA VAL B1094 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.38e+00 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.46e+00 ... (remaining 21909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29215 2.44 - 4.89: 517 4.89 - 7.33: 44 7.33 - 9.77: 11 9.77 - 12.21: 3 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C ILE B 834 " pdb=" N LYS B 835 " pdb=" CA LYS B 835 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.08 128.65 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 115.79 110.48 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ASN B1098 " pdb=" CA ASN B1098 " pdb=" C ASN B1098 " ideal model delta sigma weight residual 112.92 107.58 5.34 1.23e+00 6.61e-01 1.89e+01 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12464 17.93 - 35.85: 912 35.85 - 53.78: 155 53.78 - 71.70: 43 71.70 - 89.63: 24 Dihedral angle restraints: 13598 sinusoidal: 5811 harmonic: 7787 Sorted by residual: dihedral pdb=" CA CYS A1082 " pdb=" C CYS A1082 " pdb=" N HIS A1083 " pdb=" CA HIS A1083 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA ASP B 985 " pdb=" C ASP B 985 " pdb=" N LYS B 986 " pdb=" CA LYS B 986 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3501 0.143 - 0.285: 39 0.285 - 0.428: 6 0.428 - 0.571: 1 0.571 - 0.714: 1 Chirality restraints: 3548 Sorted by residual: chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C2 NAG B1208 " pdb=" C1 NAG B1208 " pdb=" C3 NAG B1208 " pdb=" N2 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 3545 not shown) Planarity restraints: 3806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1098 " -0.027 2.00e-02 2.50e+03 2.86e-02 1.02e+01 pdb=" CG ASN B1098 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B1098 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B1098 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1206 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 633 " -0.018 2.00e-02 2.50e+03 1.98e-02 9.78e+00 pdb=" CG TRP A 633 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 633 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 633 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 633 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 633 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 633 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 633 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 633 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 633 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 295 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.036 5.00e-02 4.00e+02 ... (remaining 3803 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5194 2.80 - 3.32: 18596 3.32 - 3.85: 36361 3.85 - 4.37: 41084 4.37 - 4.90: 71700 Nonbonded interactions: 172935 Sorted by model distance: nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.270 3.040 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.299 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.301 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.309 3.040 ... (remaining 172930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 27 through 137 or resid 166 through 210 or resid 216 throu \ gh 623 or resid 638 through 677 or resid 689 through 827 or resid 854 through 11 \ 47 or resid 1201 through 1208)) selection = (chain 'C' and (resid 27 through 331 or resid 528 through 677 or resid 689 throu \ gh 1147 or resid 1201 through 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.530 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21986 Z= 0.225 Angle : 0.820 20.063 29974 Z= 0.421 Chirality : 0.056 0.714 3548 Planarity : 0.006 0.065 3775 Dihedral : 13.344 89.626 8472 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.052 0.002 TRP A 633 HIS 0.010 0.001 HIS A 519 PHE 0.040 0.002 PHE A 275 TYR 0.021 0.002 TYR A 904 ARG 0.003 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 31) link_NAG-ASN : angle 4.17733 ( 93) link_BETA1-4 : bond 0.01737 ( 9) link_BETA1-4 : angle 6.36256 ( 27) hydrogen bonds : bond 0.20363 ( 891) hydrogen bonds : angle 9.04856 ( 2496) SS BOND : bond 0.00440 ( 32) SS BOND : angle 1.58699 ( 64) covalent geometry : bond 0.00434 (21914) covalent geometry : angle 0.76143 (29790) *********************** 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 : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7392 (m-90) cc_final: 0.6961 (m-90) REVERT: B 740 MET cc_start: 0.8440 (tpp) cc_final: 0.8159 (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: 0.3652 time to fit residues: 36.3581 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 : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 919 ASN B1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.074858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.059726 restraints weight = 127378.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.060354 restraints weight = 83176.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.060658 restraints weight = 56834.751| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21986 Z= 0.126 Angle : 0.579 14.630 29974 Z= 0.294 Chirality : 0.045 0.580 3548 Planarity : 0.004 0.060 3775 Dihedral : 7.193 57.061 3679 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2622 helix: 0.74 (0.20), residues: 628 sheet: -0.06 (0.22), residues: 542 loop : -1.02 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 633 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.001 PHE C 275 TYR 0.021 0.001 TYR A1067 ARG 0.014 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 31) link_NAG-ASN : angle 2.59205 ( 93) link_BETA1-4 : bond 0.00964 ( 9) link_BETA1-4 : angle 3.77022 ( 27) hydrogen bonds : bond 0.04106 ( 891) hydrogen bonds : angle 6.51083 ( 2496) SS BOND : bond 0.00522 ( 32) SS BOND : angle 0.83086 ( 64) covalent geometry : bond 0.00263 (21914) covalent geometry : angle 0.54919 (29790) *********************** 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: 3 poor density : 49 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9259 (tp) cc_final: 0.9031 (mm) REVERT: A 633 TRP cc_start: 0.7084 (m-90) cc_final: 0.6688 (m-90) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.3328 time to fit residues: 29.8789 Evaluate side-chains 46 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 994 ASP 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 190 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 210 optimal weight: 40.0000 chunk 133 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 580 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 710 ASN B 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.072444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.057951 restraints weight = 127372.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.057716 restraints weight = 84322.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.057820 restraints weight = 70078.785| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21986 Z= 0.274 Angle : 0.728 13.823 29974 Z= 0.367 Chirality : 0.049 0.569 3548 Planarity : 0.005 0.059 3775 Dihedral : 7.342 57.054 3679 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.60 % Allowed : 6.36 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2622 helix: 0.51 (0.20), residues: 631 sheet: -0.61 (0.21), residues: 537 loop : -1.15 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 633 HIS 0.008 0.002 HIS B1048 PHE 0.025 0.002 PHE B1089 TYR 0.030 0.002 TYR C1067 ARG 0.006 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 31) link_NAG-ASN : angle 2.83676 ( 93) link_BETA1-4 : bond 0.00948 ( 9) link_BETA1-4 : angle 4.04768 ( 27) hydrogen bonds : bond 0.04820 ( 891) hydrogen bonds : angle 6.53781 ( 2496) SS BOND : bond 0.00506 ( 32) SS BOND : angle 0.95140 ( 64) covalent geometry : bond 0.00608 (21914) covalent geometry : angle 0.70091 (29790) *********************** 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 58 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 2.376 Fit side-chains REVERT: A 633 TRP cc_start: 0.7397 (m-90) cc_final: 0.7119 (m-10) REVERT: B 740 MET cc_start: 0.9021 (tpp) cc_final: 0.8727 (tpp) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 0.2884 time to fit residues: 30.0076 Evaluate side-chains 45 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 65 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 82 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 187 optimal weight: 40.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.073162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.058731 restraints weight = 129216.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.058562 restraints weight = 85054.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.058881 restraints weight = 63297.524| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21986 Z= 0.150 Angle : 0.585 13.949 29974 Z= 0.292 Chirality : 0.045 0.553 3548 Planarity : 0.004 0.052 3775 Dihedral : 7.016 57.365 3679 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.64 % Allowed : 8.11 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2622 helix: 1.05 (0.21), residues: 628 sheet: -0.54 (0.21), residues: 553 loop : -1.12 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.005 0.001 HIS B1048 PHE 0.017 0.001 PHE B 318 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 31) link_NAG-ASN : angle 2.57732 ( 93) link_BETA1-4 : bond 0.00888 ( 9) link_BETA1-4 : angle 3.83727 ( 27) hydrogen bonds : bond 0.03879 ( 891) hydrogen bonds : angle 6.08058 ( 2496) SS BOND : bond 0.00304 ( 32) SS BOND : angle 0.79144 ( 64) covalent geometry : bond 0.00324 (21914) covalent geometry : angle 0.55601 (29790) *********************** 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 57 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 2.414 Fit side-chains REVERT: A 274 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 633 TRP cc_start: 0.7226 (m-90) cc_final: 0.6749 (m-10) REVERT: A 900 MET cc_start: 0.5520 (pmm) cc_final: 0.4687 (pmm) REVERT: A 1050 MET cc_start: 0.6551 (mtt) cc_final: 0.6255 (mtt) REVERT: B 233 ILE cc_start: 0.8002 (mt) cc_final: 0.7781 (mm) REVERT: B 740 MET cc_start: 0.9019 (tpp) cc_final: 0.8717 (tpp) REVERT: C 1050 MET cc_start: 0.7278 (mtm) cc_final: 0.7000 (mtm) outliers start: 15 outliers final: 9 residues processed: 54 average time/residue: 0.3092 time to fit residues: 29.6640 Evaluate side-chains 47 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 681 HIS 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 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 131 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.072607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.057932 restraints weight = 128480.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.058029 restraints weight = 90387.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.058124 restraints weight = 69498.359| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21986 Z= 0.193 Angle : 0.623 13.214 29974 Z= 0.311 Chirality : 0.046 0.540 3548 Planarity : 0.004 0.054 3775 Dihedral : 6.985 56.933 3679 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.20 % Allowed : 9.01 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2622 helix: 0.98 (0.21), residues: 636 sheet: -0.68 (0.21), residues: 539 loop : -1.11 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 633 HIS 0.007 0.001 HIS B1048 PHE 0.017 0.002 PHE B1089 TYR 0.025 0.002 TYR C1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 31) link_NAG-ASN : angle 2.56629 ( 93) link_BETA1-4 : bond 0.00842 ( 9) link_BETA1-4 : angle 3.80235 ( 27) hydrogen bonds : bond 0.04012 ( 891) hydrogen bonds : angle 6.05791 ( 2496) SS BOND : bond 0.00388 ( 32) SS BOND : angle 1.05577 ( 64) covalent geometry : bond 0.00425 (21914) covalent geometry : angle 0.59569 (29790) *********************** 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 70 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 2.371 Fit side-chains REVERT: A 374 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.6209 (p90) REVERT: B 740 MET cc_start: 0.9022 (tpp) cc_final: 0.8724 (tpp) outliers start: 28 outliers final: 19 residues processed: 67 average time/residue: 0.2850 time to fit residues: 34.2601 Evaluate side-chains 57 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 681 HIS 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 994 ASP 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 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 100 optimal weight: 6.9990 chunk 198 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.072440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.057528 restraints weight = 128180.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.057655 restraints weight = 89414.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.057755 restraints weight = 66304.938| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2511 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= 0.219 Angle : 0.646 10.980 29974 Z= 0.321 Chirality : 0.046 0.361 3548 Planarity : 0.004 0.055 3775 Dihedral : 7.343 82.919 3679 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.15 % Allowed : 10.12 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2622 helix: 0.92 (0.20), residues: 636 sheet: -0.95 (0.21), residues: 521 loop : -1.11 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1102 HIS 0.007 0.001 HIS B1048 PHE 0.017 0.002 PHE B1089 TYR 0.028 0.002 TYR C1067 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 31) link_NAG-ASN : angle 2.54270 ( 93) link_BETA1-4 : bond 0.00848 ( 9) link_BETA1-4 : angle 3.81670 ( 27) hydrogen bonds : bond 0.04069 ( 891) hydrogen bonds : angle 6.10118 ( 2496) SS BOND : bond 0.00450 ( 32) SS BOND : angle 0.93811 ( 64) covalent geometry : bond 0.00482 (21914) covalent geometry : angle 0.62059 (29790) *********************** 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 68 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 2.355 Fit side-chains REVERT: A 374 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6196 (p90) REVERT: B 740 MET cc_start: 0.9013 (tpp) cc_final: 0.8711 (tpp) outliers start: 27 outliers final: 19 residues processed: 65 average time/residue: 0.2863 time to fit residues: 33.3968 Evaluate side-chains 57 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 681 HIS 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 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 770 ILE 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 93 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 234 optimal weight: 0.0030 chunk 130 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 137 ASN B 804 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.089108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.068974 restraints weight = 82640.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.068916 restraints weight = 72474.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.068574 restraints weight = 71298.059| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2472 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= 0.116 Angle : 0.553 10.628 29974 Z= 0.274 Chirality : 0.044 0.351 3548 Planarity : 0.004 0.053 3775 Dihedral : 7.007 83.270 3679 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.07 % Allowed : 10.59 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2622 helix: 1.38 (0.21), residues: 635 sheet: -0.51 (0.22), residues: 536 loop : -1.07 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 PHE 0.014 0.001 PHE B 318 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 31) link_NAG-ASN : angle 2.28058 ( 93) link_BETA1-4 : bond 0.00964 ( 9) link_BETA1-4 : angle 3.66172 ( 27) hydrogen bonds : bond 0.03528 ( 891) hydrogen bonds : angle 5.69498 ( 2496) SS BOND : bond 0.00238 ( 32) SS BOND : angle 0.69552 ( 64) covalent geometry : bond 0.00249 (21914) covalent geometry : angle 0.52714 (29790) *********************** 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 68 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 2.467 Fit side-chains REVERT: A 374 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5863 (p90) REVERT: B 740 MET cc_start: 0.8950 (tpp) cc_final: 0.8654 (tpp) outliers start: 25 outliers final: 16 residues processed: 63 average time/residue: 0.3129 time to fit residues: 34.0876 Evaluate side-chains 55 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 681 HIS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 209 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 224 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.072096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057702 restraints weight = 129036.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057263 restraints weight = 84167.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057437 restraints weight = 70921.026| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21986 Z= 0.246 Angle : 0.670 11.006 29974 Z= 0.334 Chirality : 0.046 0.300 3548 Planarity : 0.004 0.055 3775 Dihedral : 7.271 82.582 3679 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.32 % Allowed : 10.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2622 helix: 0.96 (0.21), residues: 634 sheet: -0.92 (0.22), residues: 513 loop : -1.10 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1102 HIS 0.007 0.001 HIS B1048 PHE 0.022 0.002 PHE B1089 TYR 0.037 0.002 TYR A 449 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 31) link_NAG-ASN : angle 2.46483 ( 93) link_BETA1-4 : bond 0.00841 ( 9) link_BETA1-4 : angle 3.80537 ( 27) hydrogen bonds : bond 0.04169 ( 891) hydrogen bonds : angle 6.05653 ( 2496) SS BOND : bond 0.00498 ( 32) SS BOND : angle 0.89565 ( 64) covalent geometry : bond 0.00545 (21914) covalent geometry : angle 0.64656 (29790) *********************** 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 73 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6126 (p90) REVERT: B 740 MET cc_start: 0.8995 (tpp) cc_final: 0.8704 (tpp) outliers start: 31 outliers final: 26 residues processed: 70 average time/residue: 0.2897 time to fit residues: 36.3847 Evaluate side-chains 67 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 501 TYR 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 681 HIS 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 277 LEU 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 994 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 174 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3963 r_free = 0.3963 target = 0.072250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.057269 restraints weight = 128302.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.057680 restraints weight = 78523.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.057739 restraints weight = 59852.004| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21986 Z= 0.209 Angle : 0.634 11.226 29974 Z= 0.315 Chirality : 0.046 0.282 3548 Planarity : 0.004 0.056 3775 Dihedral : 7.235 81.173 3679 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.28 % Allowed : 10.97 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2622 helix: 1.00 (0.21), residues: 633 sheet: -0.93 (0.22), residues: 502 loop : -1.14 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1102 HIS 0.007 0.001 HIS B1048 PHE 0.018 0.002 PHE B1089 TYR 0.028 0.002 TYR C1067 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 31) link_NAG-ASN : angle 2.37977 ( 93) link_BETA1-4 : bond 0.00923 ( 9) link_BETA1-4 : angle 3.77807 ( 27) hydrogen bonds : bond 0.03982 ( 891) hydrogen bonds : angle 5.99542 ( 2496) SS BOND : bond 0.00425 ( 32) SS BOND : angle 0.85517 ( 64) covalent geometry : bond 0.00462 (21914) covalent geometry : angle 0.60994 (29790) *********************** 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 70 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 2.414 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6060 (p90) REVERT: B 740 MET cc_start: 0.8985 (tpp) cc_final: 0.8699 (tpp) outliers start: 30 outliers final: 27 residues processed: 67 average time/residue: 0.3146 time to fit residues: 37.4101 Evaluate side-chains 66 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 501 TYR 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 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 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 994 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.0980 chunk 25 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 710 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.073810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.059591 restraints weight = 129892.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.059584 restraints weight = 83006.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.059870 restraints weight = 61943.501| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21986 Z= 0.097 Angle : 0.538 10.746 29974 Z= 0.267 Chirality : 0.044 0.259 3548 Planarity : 0.004 0.057 3775 Dihedral : 6.668 76.134 3679 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.98 % Allowed : 11.27 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2622 helix: 1.66 (0.21), residues: 629 sheet: -0.53 (0.22), residues: 545 loop : -0.97 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1102 HIS 0.005 0.001 HIS B1048 PHE 0.014 0.001 PHE B 318 TYR 0.030 0.001 TYR A 449 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 31) link_NAG-ASN : angle 1.95807 ( 93) link_BETA1-4 : bond 0.01045 ( 9) link_BETA1-4 : angle 3.61791 ( 27) hydrogen bonds : bond 0.03337 ( 891) hydrogen bonds : angle 5.45925 ( 2496) SS BOND : bond 0.00162 ( 32) SS BOND : angle 0.69206 ( 64) covalent geometry : bond 0.00205 (21914) covalent geometry : angle 0.51618 (29790) ********************** 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 71 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 2.352 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5909 (p90) REVERT: B 740 MET cc_start: 0.9008 (tpp) cc_final: 0.8728 (tpp) outliers start: 23 outliers final: 18 residues processed: 67 average time/residue: 0.3049 time to fit residues: 36.2018 Evaluate side-chains 60 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1082 CYS 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 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 223 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 481 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.090490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.069718 restraints weight = 79678.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.069955 restraints weight = 71643.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.069186 restraints weight = 69228.155| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21986 Z= 0.131 Angle : 0.556 10.440 29974 Z= 0.276 Chirality : 0.044 0.253 3548 Planarity : 0.004 0.052 3775 Dihedral : 6.670 75.127 3679 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.77 % Allowed : 11.53 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2622 helix: 1.57 (0.21), residues: 636 sheet: -0.51 (0.22), residues: 537 loop : -0.98 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1102 HIS 0.005 0.001 HIS B1048 PHE 0.013 0.001 PHE B 318 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 31) link_NAG-ASN : angle 2.01210 ( 93) link_BETA1-4 : bond 0.00984 ( 9) link_BETA1-4 : angle 3.60250 ( 27) hydrogen bonds : bond 0.03496 ( 891) hydrogen bonds : angle 5.50031 ( 2496) SS BOND : bond 0.00386 ( 32) SS BOND : angle 0.91084 ( 64) covalent geometry : bond 0.00287 (21914) covalent geometry : angle 0.53374 (29790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5557.10 seconds wall clock time: 98 minutes 45.69 seconds (5925.69 seconds total)