Starting phenix.real_space_refine on Thu Mar 5 23:18:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgx_25888/03_2026/7tgx_25888.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 116 5.16 5 C 16430 2.51 5 N 4251 2.21 5 O 4981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25778 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 8451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8451 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 53, 'TRANS': 1027} Chain breaks: 5 Chain: "A" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8459 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 53, 'TRANS': 1028} Chain breaks: 5 Chain: "B" Number of atoms: 8435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8435 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 53, 'TRANS': 1027} Chain breaks: 5 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 81 Unusual residues: {'MAN': 1, 'NAG': 5} 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.07, per 1000 atoms: 0.24 Number of scatterers: 25778 At special positions: 0 Unit cell: (151.3, 158.42, 202.03, 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 116 16.00 O 4981 8.00 N 4251 7.00 C 16430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 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 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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 ALPHA1-4 " NAG D 1 " - " MAN D 2 " " NAG E 1 " - " MAN E 2 " " NAG F 1 " - " MAN F 2 " " NAG H 1 " - " MAN H 2 " MAN-ASN " MAN C1302 " - " ASN C 717 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A1134 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG C1301 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 616 " " NAG D 1 " - " ASN C1134 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG H 1 " - " ASN C 801 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6070 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 43 sheets defined 25.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.861A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.727A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.435A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.535A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.579A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.891A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 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: 3.553A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.649A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.679A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.513A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.625A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.506A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.078A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.570A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.257A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 4.139A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.657A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.565A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.731A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.681A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.870A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.580A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.579A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.098A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.533A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.511A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.428A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.659A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.742A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.900A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.665A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.726A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.564A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.833A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.652A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.568A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.601A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.645A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.579A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.033A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.703A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.877A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.685A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.002A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.026A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.207A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.443A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.190A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.495A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.691A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.658A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 715 removed outlier: 4.801A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 719 through 728 removed outlier: 6.043A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.910A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HIS A 69 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY A 261 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.272A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.124A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.481A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.474A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.812A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.534A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.649A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.122A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.902A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.538A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 11.731A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.298A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.227A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.343A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.060A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.572A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8197 1.34 - 1.46: 6401 1.46 - 1.59: 11622 1.59 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 26366 Sorted by residual: bond pdb=" N CYS C 851 " pdb=" CA CYS C 851 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.35e-02 5.49e+03 1.02e+01 bond pdb=" N ILE C 850 " pdb=" CA ILE C 850 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.07e-02 8.73e+03 1.01e+01 bond pdb=" C1 MAN E 2 " pdb=" C2 MAN E 2 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" CA ILE C 850 " pdb=" C ILE C 850 " ideal model delta sigma weight residual 1.521 1.550 -0.029 1.26e-02 6.30e+03 5.40e+00 bond pdb=" C ILE C 850 " pdb=" O ILE C 850 " ideal model delta sigma weight residual 1.232 1.264 -0.032 1.44e-02 4.82e+03 4.83e+00 ... (remaining 26361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 35406 2.45 - 4.89: 437 4.89 - 7.34: 27 7.34 - 9.78: 4 9.78 - 12.23: 2 Bond angle restraints: 35876 Sorted by residual: angle pdb=" C LEU C 849 " pdb=" N ILE C 850 " pdb=" CA ILE C 850 " ideal model delta sigma weight residual 122.11 134.34 -12.23 1.12e+00 7.97e-01 1.19e+02 angle pdb=" CA GLN C 853 " pdb=" CB GLN C 853 " pdb=" CG GLN C 853 " ideal model delta sigma weight residual 114.10 124.29 -10.19 2.00e+00 2.50e-01 2.60e+01 angle pdb=" O LEU C 849 " pdb=" C LEU C 849 " pdb=" N ILE C 850 " ideal model delta sigma weight residual 123.00 131.14 -8.14 1.60e+00 3.91e-01 2.59e+01 angle pdb=" CA PHE C 855 " pdb=" C PHE C 855 " pdb=" N ASN C 856 " ideal model delta sigma weight residual 118.22 122.18 -3.96 1.03e+00 9.43e-01 1.48e+01 angle pdb=" CA ILE C 850 " pdb=" C ILE C 850 " pdb=" O ILE C 850 " ideal model delta sigma weight residual 121.09 118.13 2.96 8.20e-01 1.49e+00 1.31e+01 ... (remaining 35871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 15226 25.03 - 50.06: 734 50.06 - 75.09: 97 75.09 - 100.12: 42 100.12 - 125.15: 22 Dihedral angle restraints: 16121 sinusoidal: 6684 harmonic: 9437 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.53 87.53 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -141.72 -38.28 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 144.08 35.92 0 5.00e+00 4.00e-02 5.16e+01 ... (remaining 16118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3209 0.052 - 0.104: 759 0.104 - 0.156: 173 0.156 - 0.207: 6 0.207 - 0.259: 8 Chirality restraints: 4155 Sorted by residual: chirality pdb=" C1 MAN F 2 " pdb=" O4 NAG F 1 " pdb=" C2 MAN F 2 " pdb=" O5 MAN F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.50e+00 chirality pdb=" C1 MAN D 2 " pdb=" O4 NAG D 1 " pdb=" C2 MAN D 2 " pdb=" O5 MAN D 2 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.91e+00 chirality pdb=" C1 MAN E 2 " pdb=" O4 NAG E 1 " pdb=" C2 MAN E 2 " pdb=" O5 MAN E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.22e+00 ... (remaining 4152 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 82 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " 0.025 2.00e-02 2.50e+03 2.29e-02 6.54e+00 pdb=" CG ASN C 801 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 515 " 0.013 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE A 515 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 515 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 515 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 515 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 515 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 515 " 0.005 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 170 2.54 - 3.13: 20335 3.13 - 3.72: 34626 3.72 - 4.31: 49589 4.31 - 4.90: 86449 Nonbonded interactions: 191169 Sorted by model distance: nonbonded pdb=" O3 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 1.948 3.040 nonbonded pdb=" O3 NAG B1302 " pdb=" O7 NAG B1302 " model vdw 1.998 3.040 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.022 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.033 3.120 nonbonded pdb=" O LYS B 97 " pdb=" OG SER B 98 " model vdw 2.069 3.040 ... (remaining 191164 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 'A' and (resid 14 through 622 or resid 635 through 828 or resid 834 or re \ sid 852 through 1148 or resid 1301 or resid 1303 through 1306)) selection = (chain 'B' and (resid 14 through 622 or resid 635 through 828 or resid 834 or re \ sid 852 through 1148 or resid 1302 or resid 1304 through 1307)) selection = (chain 'C' and (resid 14 through 622 or resid 635 through 828 or resid 850 or re \ sid 852 through 1148 or resid 1301 or resid 1303 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.940 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26440 Z= 0.237 Angle : 0.698 12.227 36055 Z= 0.378 Chirality : 0.048 0.259 4155 Planarity : 0.005 0.064 4605 Dihedral : 15.447 125.148 9925 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.25 % Allowed : 0.81 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3208 helix: 0.25 (0.21), residues: 657 sheet: -0.33 (0.19), residues: 652 loop : -2.59 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.020 0.001 TYR A 266 PHE 0.037 0.002 PHE A 515 TRP 0.020 0.002 TRP B 258 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00528 (26366) covalent geometry : angle 0.68096 (35876) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.74277 ( 84) hydrogen bonds : bond 0.14944 ( 984) hydrogen bonds : angle 6.79309 ( 2670) link_ALPHA1-4 : bond 0.00675 ( 4) link_ALPHA1-4 : angle 2.48374 ( 12) link_MAN-ASN : bond 0.00200 ( 1) link_MAN-ASN : angle 1.13656 ( 2) link_NAG-ASN : bond 0.00311 ( 27) link_NAG-ASN : angle 2.74635 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8503 (pp20) REVERT: A 515 PHE cc_start: 0.7694 (p90) cc_final: 0.7231 (p90) REVERT: A 745 ASP cc_start: 0.7866 (t0) cc_final: 0.7561 (t0) REVERT: A 854 LYS cc_start: 0.6061 (mptt) cc_final: 0.5808 (mptt) REVERT: B 104 TRP cc_start: 0.7516 (m-90) cc_final: 0.6900 (m-90) outliers start: 7 outliers final: 4 residues processed: 125 average time/residue: 0.1657 time to fit residues: 34.8464 Evaluate side-chains 85 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1134 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 ASN C 914 ASN A 14 GLN A 121 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.107513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064783 restraints weight = 64527.426| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.78 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26440 Z= 0.191 Angle : 0.678 9.420 36055 Z= 0.347 Chirality : 0.049 0.365 4155 Planarity : 0.005 0.049 4605 Dihedral : 10.763 114.511 4142 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.57 % Allowed : 5.52 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3208 helix: 0.85 (0.21), residues: 670 sheet: 0.03 (0.19), residues: 655 loop : -2.34 (0.12), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 78 TYR 0.021 0.001 TYR A 266 PHE 0.027 0.002 PHE A 157 TRP 0.015 0.001 TRP C 152 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00451 (26366) covalent geometry : angle 0.65635 (35876) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.43891 ( 84) hydrogen bonds : bond 0.07511 ( 984) hydrogen bonds : angle 5.52897 ( 2670) link_ALPHA1-4 : bond 0.01151 ( 4) link_ALPHA1-4 : angle 2.95891 ( 12) link_MAN-ASN : bond 0.00539 ( 1) link_MAN-ASN : angle 1.63997 ( 2) link_NAG-ASN : bond 0.00461 ( 27) link_NAG-ASN : angle 3.23420 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.994 Fit side-chains REVERT: A 340 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8417 (pp20) REVERT: A 515 PHE cc_start: 0.7771 (p90) cc_final: 0.7493 (p90) REVERT: A 745 ASP cc_start: 0.8452 (t0) cc_final: 0.8150 (t0) REVERT: A 854 LYS cc_start: 0.5981 (mptt) cc_final: 0.5535 (mptt) REVERT: B 104 TRP cc_start: 0.7625 (m-90) cc_final: 0.7128 (m-90) REVERT: B 417 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8975 (ttpt) REVERT: B 571 ASP cc_start: 0.8835 (t0) cc_final: 0.8618 (t0) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 0.1622 time to fit residues: 28.0807 Evaluate side-chains 89 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 110 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 606 ASN A 14 GLN A 580 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068271 restraints weight = 66790.460| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.89 r_work: 0.2841 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26440 Z= 0.170 Angle : 0.618 8.792 36055 Z= 0.317 Chirality : 0.047 0.312 4155 Planarity : 0.004 0.055 4605 Dihedral : 9.597 105.641 4137 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.78 % Allowed : 8.31 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3208 helix: 1.26 (0.21), residues: 662 sheet: 0.15 (0.20), residues: 626 loop : -2.10 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE A 392 TRP 0.013 0.001 TRP C 152 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (26366) covalent geometry : angle 0.59885 (35876) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.26804 ( 84) hydrogen bonds : bond 0.07027 ( 984) hydrogen bonds : angle 5.25631 ( 2670) link_ALPHA1-4 : bond 0.01073 ( 4) link_ALPHA1-4 : angle 2.77276 ( 12) link_MAN-ASN : bond 0.00101 ( 1) link_MAN-ASN : angle 2.55198 ( 2) link_NAG-ASN : bond 0.00430 ( 27) link_NAG-ASN : angle 2.81785 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: C 855 PHE cc_start: 0.7816 (m-10) cc_final: 0.7581 (m-80) REVERT: A 340 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8452 (pp20) REVERT: A 515 PHE cc_start: 0.7705 (p90) cc_final: 0.7142 (p90) REVERT: A 745 ASP cc_start: 0.8549 (t0) cc_final: 0.8236 (t0) REVERT: B 104 TRP cc_start: 0.7638 (m-90) cc_final: 0.7157 (m-90) REVERT: B 417 LYS cc_start: 0.9276 (mtpt) cc_final: 0.9047 (ttpt) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.1564 time to fit residues: 27.9245 Evaluate side-chains 101 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 182 optimal weight: 0.0000 chunk 265 optimal weight: 2.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A1119 ASN B 519 HIS B 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.112753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069212 restraints weight = 66215.566| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.90 r_work: 0.2869 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26440 Z= 0.135 Angle : 0.577 8.375 36055 Z= 0.294 Chirality : 0.046 0.305 4155 Planarity : 0.004 0.057 4605 Dihedral : 8.139 97.318 4137 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.99 % Allowed : 9.79 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3208 helix: 1.59 (0.21), residues: 662 sheet: 0.24 (0.20), residues: 613 loop : -1.92 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.018 0.001 TYR C1067 PHE 0.028 0.001 PHE A 392 TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (26366) covalent geometry : angle 0.55966 (35876) SS BOND : bond 0.00299 ( 42) SS BOND : angle 1.09523 ( 84) hydrogen bonds : bond 0.06122 ( 984) hydrogen bonds : angle 5.02019 ( 2670) link_ALPHA1-4 : bond 0.01667 ( 4) link_ALPHA1-4 : angle 2.85071 ( 12) link_MAN-ASN : bond 0.00017 ( 1) link_MAN-ASN : angle 1.58221 ( 2) link_NAG-ASN : bond 0.00361 ( 27) link_NAG-ASN : angle 2.61097 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 855 PHE cc_start: 0.7912 (m-10) cc_final: 0.7697 (m-80) REVERT: A 340 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8449 (pp20) REVERT: A 745 ASP cc_start: 0.8474 (t0) cc_final: 0.8273 (t0) REVERT: B 104 TRP cc_start: 0.7636 (m-90) cc_final: 0.7217 (m-90) REVERT: B 137 ASN cc_start: 0.8678 (m-40) cc_final: 0.7962 (p0) REVERT: B 417 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9076 (ttpt) REVERT: B 571 ASP cc_start: 0.8948 (t0) cc_final: 0.8574 (t0) outliers start: 28 outliers final: 15 residues processed: 123 average time/residue: 0.1529 time to fit residues: 32.4394 Evaluate side-chains 109 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 281 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1083 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.111187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067557 restraints weight = 66168.348| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.87 r_work: 0.2829 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26440 Z= 0.187 Angle : 0.608 9.362 36055 Z= 0.312 Chirality : 0.046 0.300 4155 Planarity : 0.004 0.056 4605 Dihedral : 7.788 90.416 4136 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.59 % Allowed : 11.03 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3208 helix: 1.53 (0.21), residues: 662 sheet: 0.32 (0.20), residues: 604 loop : -1.91 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.019 0.001 TYR C1067 PHE 0.015 0.001 PHE A 906 TRP 0.013 0.001 TRP A 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00447 (26366) covalent geometry : angle 0.59070 (35876) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.27858 ( 84) hydrogen bonds : bond 0.07015 ( 984) hydrogen bonds : angle 5.08447 ( 2670) link_ALPHA1-4 : bond 0.01359 ( 4) link_ALPHA1-4 : angle 2.68694 ( 12) link_MAN-ASN : bond 0.00268 ( 1) link_MAN-ASN : angle 1.57534 ( 2) link_NAG-ASN : bond 0.00368 ( 27) link_NAG-ASN : angle 2.64496 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.0451 (ptt) cc_final: 0.0233 (ptt) REVERT: C 515 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7132 (p90) REVERT: A 340 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8463 (pp20) REVERT: A 365 TYR cc_start: 0.9260 (m-10) cc_final: 0.9044 (m-10) REVERT: A 790 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9097 (ptpp) REVERT: B 104 TRP cc_start: 0.7651 (m-90) cc_final: 0.7221 (m-90) REVERT: B 137 ASN cc_start: 0.8811 (m-40) cc_final: 0.8096 (p0) REVERT: B 417 LYS cc_start: 0.9285 (mtpt) cc_final: 0.9068 (ttpt) outliers start: 45 outliers final: 31 residues processed: 132 average time/residue: 0.1578 time to fit residues: 35.3769 Evaluate side-chains 121 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 115 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 281 optimal weight: 0.4980 chunk 305 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.112835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069587 restraints weight = 66569.479| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.89 r_work: 0.2867 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26440 Z= 0.126 Angle : 0.565 9.232 36055 Z= 0.288 Chirality : 0.045 0.268 4155 Planarity : 0.004 0.057 4605 Dihedral : 7.318 88.904 4136 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.17 % Allowed : 11.81 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3208 helix: 1.80 (0.21), residues: 658 sheet: 0.34 (0.20), residues: 626 loop : -1.83 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.017 0.001 TYR C1067 PHE 0.015 0.001 PHE A 157 TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00281 (26366) covalent geometry : angle 0.55015 (35876) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.01592 ( 84) hydrogen bonds : bond 0.06012 ( 984) hydrogen bonds : angle 4.90601 ( 2670) link_ALPHA1-4 : bond 0.01517 ( 4) link_ALPHA1-4 : angle 2.29358 ( 12) link_MAN-ASN : bond 0.00065 ( 1) link_MAN-ASN : angle 1.21793 ( 2) link_NAG-ASN : bond 0.00394 ( 27) link_NAG-ASN : angle 2.47604 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: C 855 PHE cc_start: 0.7875 (m-80) cc_final: 0.7652 (m-80) REVERT: A 340 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8467 (pp20) REVERT: A 346 ARG cc_start: 0.8463 (tmt170) cc_final: 0.8166 (tmt170) REVERT: B 104 TRP cc_start: 0.7617 (m-90) cc_final: 0.7232 (m-90) REVERT: B 135 PHE cc_start: 0.8485 (m-80) cc_final: 0.8268 (m-80) REVERT: B 137 ASN cc_start: 0.8836 (m-40) cc_final: 0.8072 (p0) REVERT: B 571 ASP cc_start: 0.8917 (t0) cc_final: 0.8605 (t0) REVERT: B 878 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8732 (mt) outliers start: 33 outliers final: 26 residues processed: 122 average time/residue: 0.1457 time to fit residues: 30.4717 Evaluate side-chains 119 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 161 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 33 optimal weight: 0.0980 chunk 314 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.114057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071095 restraints weight = 65861.153| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.86 r_work: 0.2906 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26440 Z= 0.106 Angle : 0.542 10.194 36055 Z= 0.275 Chirality : 0.044 0.258 4155 Planarity : 0.004 0.057 4605 Dihedral : 6.675 84.657 4136 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.38 % Allowed : 11.99 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3208 helix: 1.90 (0.21), residues: 672 sheet: 0.40 (0.20), residues: 634 loop : -1.73 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.016 0.001 TYR C1067 PHE 0.014 0.001 PHE C 133 TRP 0.010 0.001 TRP C 152 HIS 0.005 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00225 (26366) covalent geometry : angle 0.52865 (35876) SS BOND : bond 0.00260 ( 42) SS BOND : angle 0.88130 ( 84) hydrogen bonds : bond 0.05193 ( 984) hydrogen bonds : angle 4.70674 ( 2670) link_ALPHA1-4 : bond 0.01583 ( 4) link_ALPHA1-4 : angle 2.02048 ( 12) link_MAN-ASN : bond 0.00002 ( 1) link_MAN-ASN : angle 0.99783 ( 2) link_NAG-ASN : bond 0.00365 ( 27) link_NAG-ASN : angle 2.33771 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 855 PHE cc_start: 0.7859 (m-80) cc_final: 0.7636 (m-80) REVERT: A 340 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8478 (pp20) REVERT: A 387 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 790 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9074 (mtmm) REVERT: B 104 TRP cc_start: 0.7594 (m-90) cc_final: 0.7216 (m-90) REVERT: B 137 ASN cc_start: 0.8853 (m-40) cc_final: 0.8101 (p0) REVERT: B 571 ASP cc_start: 0.8926 (t0) cc_final: 0.8600 (t0) outliers start: 39 outliers final: 27 residues processed: 129 average time/residue: 0.1513 time to fit residues: 33.2032 Evaluate side-chains 121 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 182 optimal weight: 0.0040 chunk 13 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070122 restraints weight = 66549.841| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.91 r_work: 0.2880 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26440 Z= 0.124 Angle : 0.543 8.397 36055 Z= 0.278 Chirality : 0.044 0.332 4155 Planarity : 0.004 0.056 4605 Dihedral : 6.572 86.116 4136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.20 % Allowed : 12.38 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3208 helix: 1.89 (0.21), residues: 676 sheet: 0.48 (0.20), residues: 624 loop : -1.71 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.017 0.001 TYR C1067 PHE 0.028 0.001 PHE A 392 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00284 (26366) covalent geometry : angle 0.52938 (35876) SS BOND : bond 0.00274 ( 42) SS BOND : angle 0.97505 ( 84) hydrogen bonds : bond 0.05640 ( 984) hydrogen bonds : angle 4.71846 ( 2670) link_ALPHA1-4 : bond 0.01367 ( 4) link_ALPHA1-4 : angle 1.91592 ( 12) link_MAN-ASN : bond 0.00120 ( 1) link_MAN-ASN : angle 1.04124 ( 2) link_NAG-ASN : bond 0.00344 ( 27) link_NAG-ASN : angle 2.38220 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: C 158 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6095 (mmp80) REVERT: A 340 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8479 (pp20) REVERT: A 346 ARG cc_start: 0.8461 (tmt170) cc_final: 0.8167 (tmt170) REVERT: A 387 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 790 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9091 (mtmm) REVERT: B 104 TRP cc_start: 0.7610 (m-90) cc_final: 0.7213 (m-90) REVERT: B 137 ASN cc_start: 0.8877 (m-40) cc_final: 0.8095 (p0) REVERT: B 417 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8993 (tttt) REVERT: B 571 ASP cc_start: 0.8936 (t0) cc_final: 0.8507 (t0) outliers start: 34 outliers final: 25 residues processed: 129 average time/residue: 0.1563 time to fit residues: 34.2821 Evaluate side-chains 124 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 80 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 152 optimal weight: 40.0000 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 291 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.107580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065002 restraints weight = 64111.669| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.77 r_work: 0.2861 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26440 Z= 0.152 Angle : 0.564 8.462 36055 Z= 0.289 Chirality : 0.045 0.276 4155 Planarity : 0.004 0.056 4605 Dihedral : 6.612 86.983 4136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.34 % Allowed : 12.34 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3208 helix: 1.84 (0.21), residues: 675 sheet: 0.44 (0.20), residues: 619 loop : -1.71 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.018 0.001 TYR C1067 PHE 0.012 0.001 PHE A 157 TRP 0.014 0.001 TRP A 886 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00356 (26366) covalent geometry : angle 0.55037 (35876) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.10348 ( 84) hydrogen bonds : bond 0.06247 ( 984) hydrogen bonds : angle 4.80262 ( 2670) link_ALPHA1-4 : bond 0.01146 ( 4) link_ALPHA1-4 : angle 1.91136 ( 12) link_MAN-ASN : bond 0.00225 ( 1) link_MAN-ASN : angle 1.17994 ( 2) link_NAG-ASN : bond 0.00333 ( 27) link_NAG-ASN : angle 2.39377 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1017 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8615 (tt0) REVERT: A 340 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8497 (pp20) REVERT: A 346 ARG cc_start: 0.8468 (tmt170) cc_final: 0.8152 (tmt170) REVERT: A 387 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 104 TRP cc_start: 0.7603 (m-90) cc_final: 0.7202 (m-90) REVERT: B 137 ASN cc_start: 0.8926 (m-40) cc_final: 0.8137 (p0) REVERT: B 571 ASP cc_start: 0.8968 (t0) cc_final: 0.8631 (t0) outliers start: 38 outliers final: 30 residues processed: 128 average time/residue: 0.1572 time to fit residues: 34.1759 Evaluate side-chains 125 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 248 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 143 optimal weight: 6.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.106674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062283 restraints weight = 66103.479| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.91 r_work: 0.2799 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 26440 Z= 0.233 Angle : 0.625 8.207 36055 Z= 0.323 Chirality : 0.047 0.309 4155 Planarity : 0.004 0.054 4605 Dihedral : 6.952 92.224 4136 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.17 % Allowed : 12.62 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3208 helix: 1.64 (0.21), residues: 675 sheet: 0.23 (0.20), residues: 641 loop : -1.77 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.020 0.001 TYR C1067 PHE 0.017 0.002 PHE A 92 TRP 0.019 0.001 TRP C 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00567 (26366) covalent geometry : angle 0.60946 (35876) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.36802 ( 84) hydrogen bonds : bond 0.07505 ( 984) hydrogen bonds : angle 5.06321 ( 2670) link_ALPHA1-4 : bond 0.00994 ( 4) link_ALPHA1-4 : angle 1.93284 ( 12) link_MAN-ASN : bond 0.00495 ( 1) link_MAN-ASN : angle 1.40632 ( 2) link_NAG-ASN : bond 0.00342 ( 27) link_NAG-ASN : angle 2.60543 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1017 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8621 (tt0) REVERT: A 340 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8485 (pp20) REVERT: A 346 ARG cc_start: 0.8460 (tmt170) cc_final: 0.8150 (tmt170) REVERT: A 387 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8714 (mt) REVERT: B 104 TRP cc_start: 0.7652 (m-90) cc_final: 0.7212 (m-90) REVERT: B 137 ASN cc_start: 0.8979 (m-40) cc_final: 0.8189 (p0) REVERT: B 571 ASP cc_start: 0.8991 (t0) cc_final: 0.8649 (t0) outliers start: 33 outliers final: 28 residues processed: 119 average time/residue: 0.1444 time to fit residues: 29.0869 Evaluate side-chains 118 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 312 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 181 optimal weight: 0.2980 chunk 136 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.070388 restraints weight = 65968.824| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.88 r_work: 0.2889 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26440 Z= 0.110 Angle : 0.550 8.423 36055 Z= 0.281 Chirality : 0.044 0.288 4155 Planarity : 0.004 0.057 4605 Dihedral : 6.379 80.435 4136 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.92 % Allowed : 13.22 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3208 helix: 1.91 (0.21), residues: 676 sheet: 0.46 (0.20), residues: 613 loop : -1.67 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.016 0.001 TYR C1067 PHE 0.013 0.001 PHE C 133 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00231 (26366) covalent geometry : angle 0.53745 (35876) SS BOND : bond 0.00264 ( 42) SS BOND : angle 0.90672 ( 84) hydrogen bonds : bond 0.05495 ( 984) hydrogen bonds : angle 4.73471 ( 2670) link_ALPHA1-4 : bond 0.01101 ( 4) link_ALPHA1-4 : angle 2.00962 ( 12) link_MAN-ASN : bond 0.00003 ( 1) link_MAN-ASN : angle 0.99817 ( 2) link_NAG-ASN : bond 0.00364 ( 27) link_NAG-ASN : angle 2.32613 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7110.96 seconds wall clock time: 122 minutes 10.11 seconds (7330.11 seconds total)