Starting phenix.real_space_refine on Sun Jun 22 16:43:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgx_25888/06_2025/7tgx_25888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgx_25888/06_2025/7tgx_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_25888/06_2025/7tgx_25888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgx_25888/06_2025/7tgx_25888.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgx_25888/06_2025/7tgx_25888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgx_25888/06_2025/7tgx_25888.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.39, per 1000 atoms: 0.60 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: 6.04 Conformation dependent library (CDL) restraints added in 3.4 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: 3.57 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: 11.52 Time building geometry restraints manager: 7.28 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.910 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.140 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- 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 : 7.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP B 258 HIS 0.005 0.001 HIS A1083 PHE 0.037 0.002 PHE A 515 TYR 0.020 0.001 TYR A 266 ARG 0.007 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 27) link_NAG-ASN : angle 2.74635 ( 81) link_ALPHA1-4 : bond 0.00675 ( 4) link_ALPHA1-4 : angle 2.48374 ( 12) hydrogen bonds : bond 0.14944 ( 984) hydrogen bonds : angle 6.79309 ( 2670) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.74277 ( 84) link_MAN-ASN : bond 0.00200 ( 1) link_MAN-ASN : angle 1.13656 ( 2) covalent geometry : bond 0.00528 (26366) covalent geometry : angle 0.68096 (35876) *********************** 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 : 2.672 Fit side-chains revert: symmetry clash 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: 0.3452 time to fit residues: 72.4477 Evaluate side-chains 87 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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 273 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 154 optimal weight: 40.0000 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 0.1980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.065493 restraints weight = 63875.609| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.81 r_work: 0.2861 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26440 Z= 0.165 Angle : 0.662 9.214 36055 Z= 0.339 Chirality : 0.048 0.353 4155 Planarity : 0.005 0.050 4605 Dihedral : 10.742 114.566 4142 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.53 % Allowed : 5.37 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3208 helix: 0.97 (0.21), residues: 663 sheet: 0.12 (0.20), residues: 650 loop : -2.32 (0.12), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 152 HIS 0.004 0.001 HIS C 69 PHE 0.026 0.001 PHE A 157 TYR 0.023 0.001 TYR A 266 ARG 0.005 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 27) link_NAG-ASN : angle 3.02097 ( 81) link_ALPHA1-4 : bond 0.01130 ( 4) link_ALPHA1-4 : angle 2.86859 ( 12) hydrogen bonds : bond 0.07203 ( 984) hydrogen bonds : angle 5.46391 ( 2670) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.35394 ( 84) link_MAN-ASN : bond 0.00510 ( 1) link_MAN-ASN : angle 1.74161 ( 2) covalent geometry : bond 0.00380 (26366) covalent geometry : angle 0.64209 (35876) *********************** 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 104 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.680 Fit side-chains REVERT: C 282 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8704 (m-40) REVERT: A 340 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8395 (pp20) REVERT: A 515 PHE cc_start: 0.7747 (p90) cc_final: 0.7478 (p90) REVERT: A 745 ASP cc_start: 0.8377 (t0) cc_final: 0.8110 (t0) REVERT: A 854 LYS cc_start: 0.5914 (mptt) cc_final: 0.5483 (mptt) REVERT: B 104 TRP cc_start: 0.7633 (m-90) cc_final: 0.7078 (m-90) REVERT: B 571 ASP cc_start: 0.8821 (t0) cc_final: 0.8601 (t0) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.3450 time to fit residues: 59.5844 Evaluate side-chains 91 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 851 CYS 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 62 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 75 optimal weight: 0.0030 chunk 149 optimal weight: 30.0000 chunk 224 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 A1119 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 919 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.110634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066854 restraints weight = 66457.777| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.87 r_work: 0.2811 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26440 Z= 0.235 Angle : 0.662 8.621 36055 Z= 0.341 Chirality : 0.048 0.328 4155 Planarity : 0.004 0.054 4605 Dihedral : 9.829 108.104 4137 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.88 % Allowed : 8.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3208 helix: 1.06 (0.20), residues: 670 sheet: 0.20 (0.20), residues: 656 loop : -2.21 (0.12), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.002 PHE A 392 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 27) link_NAG-ASN : angle 2.98773 ( 81) link_ALPHA1-4 : bond 0.00806 ( 4) link_ALPHA1-4 : angle 2.81400 ( 12) hydrogen bonds : bond 0.07842 ( 984) hydrogen bonds : angle 5.40118 ( 2670) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.46456 ( 84) link_MAN-ASN : bond 0.00046 ( 1) link_MAN-ASN : angle 2.65557 ( 2) covalent geometry : bond 0.00569 (26366) covalent geometry : angle 0.64182 (35876) *********************** 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 114 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 855 PHE cc_start: 0.7869 (m-10) cc_final: 0.7657 (m-80) REVERT: A 340 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8430 (pp20) REVERT: A 515 PHE cc_start: 0.7769 (p90) cc_final: 0.7546 (p90) REVERT: A 745 ASP cc_start: 0.8560 (t0) cc_final: 0.8284 (t0) REVERT: B 104 TRP cc_start: 0.7637 (m-90) cc_final: 0.7183 (m-90) REVERT: B 137 ASN cc_start: 0.8617 (m-40) cc_final: 0.7990 (p0) REVERT: B 417 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8954 (ttpt) REVERT: B 571 ASP cc_start: 0.8905 (t0) cc_final: 0.8629 (t0) outliers start: 25 outliers final: 18 residues processed: 109 average time/residue: 0.3289 time to fit residues: 61.6621 Evaluate side-chains 101 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ASN 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 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 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 291 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 154 optimal weight: 50.0000 chunk 101 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.112766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069210 restraints weight = 66458.446| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.92 r_work: 0.2868 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1589 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= 0.128 Angle : 0.579 8.354 36055 Z= 0.296 Chirality : 0.045 0.296 4155 Planarity : 0.004 0.057 4605 Dihedral : 8.446 101.367 4137 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.88 % Allowed : 9.69 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3208 helix: 1.53 (0.21), residues: 661 sheet: 0.29 (0.20), residues: 612 loop : -1.95 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.002 0.001 HIS C 207 PHE 0.019 0.001 PHE A 157 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 27) link_NAG-ASN : angle 2.62499 ( 81) link_ALPHA1-4 : bond 0.01625 ( 4) link_ALPHA1-4 : angle 2.65079 ( 12) hydrogen bonds : bond 0.06180 ( 984) hydrogen bonds : angle 5.05186 ( 2670) SS BOND : bond 0.00289 ( 42) SS BOND : angle 1.09424 ( 84) link_MAN-ASN : bond 0.00002 ( 1) link_MAN-ASN : angle 1.45564 ( 2) covalent geometry : bond 0.00279 (26366) covalent geometry : angle 0.56258 (35876) *********************** 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 125 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 2.921 Fit side-chains revert: symmetry clash REVERT: C 239 GLN cc_start: 0.6970 (mp-120) cc_final: 0.6535 (mp-120) REVERT: C 902 MET cc_start: 0.9218 (tpt) cc_final: 0.8895 (tpt) REVERT: A 340 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8446 (pp20) REVERT: A 745 ASP cc_start: 0.8508 (t0) cc_final: 0.8275 (t0) REVERT: B 104 TRP cc_start: 0.7633 (m-90) cc_final: 0.7217 (m-90) REVERT: B 137 ASN cc_start: 0.8686 (m-40) cc_final: 0.8006 (p0) REVERT: B 417 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8906 (ttpt) REVERT: B 878 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8710 (mt) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 0.3316 time to fit residues: 67.9232 Evaluate side-chains 111 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 242 LEU 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 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 740 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 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 210 optimal weight: 0.7980 chunk 45 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 228 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 172 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.064873 restraints weight = 64136.908| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.76 r_work: 0.2855 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26440 Z= 0.156 Angle : 0.587 9.067 36055 Z= 0.300 Chirality : 0.045 0.285 4155 Planarity : 0.004 0.057 4605 Dihedral : 7.843 91.733 4136 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.27 % Allowed : 10.93 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3208 helix: 1.59 (0.21), residues: 662 sheet: 0.38 (0.21), residues: 591 loop : -1.89 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 PHE 0.024 0.001 PHE A 392 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 27) link_NAG-ASN : angle 2.60459 ( 81) link_ALPHA1-4 : bond 0.01495 ( 4) link_ALPHA1-4 : angle 2.74855 ( 12) hydrogen bonds : bond 0.06558 ( 984) hydrogen bonds : angle 5.00423 ( 2670) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.17173 ( 84) link_MAN-ASN : bond 0.00146 ( 1) link_MAN-ASN : angle 1.46743 ( 2) covalent geometry : bond 0.00367 (26366) covalent geometry : angle 0.57008 (35876) *********************** 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 135 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 GLN cc_start: 0.7042 (mp-120) cc_final: 0.6614 (mp-120) REVERT: A 340 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8464 (pp20) REVERT: B 104 TRP cc_start: 0.7632 (m-90) cc_final: 0.7199 (m-90) REVERT: B 137 ASN cc_start: 0.8775 (m-40) cc_final: 0.8076 (p0) REVERT: B 417 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8827 (ttpt) REVERT: B 571 ASP cc_start: 0.8961 (t0) cc_final: 0.8601 (t0) outliers start: 36 outliers final: 26 residues processed: 129 average time/residue: 0.3424 time to fit residues: 75.8488 Evaluate side-chains 120 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 151 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.105483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060832 restraints weight = 66211.692| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.91 r_work: 0.2763 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 26440 Z= 0.303 Angle : 0.705 8.484 36055 Z= 0.364 Chirality : 0.049 0.312 4155 Planarity : 0.005 0.056 4605 Dihedral : 8.082 99.243 4136 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.45 % Allowed : 11.85 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3208 helix: 1.27 (0.21), residues: 662 sheet: 0.17 (0.20), residues: 630 loop : -2.00 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE A 92 TYR 0.022 0.002 TYR C1067 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 27) link_NAG-ASN : angle 2.91242 ( 81) link_ALPHA1-4 : bond 0.01234 ( 4) link_ALPHA1-4 : angle 2.68449 ( 12) hydrogen bonds : bond 0.08672 ( 984) hydrogen bonds : angle 5.39687 ( 2670) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.67355 ( 84) link_MAN-ASN : bond 0.00547 ( 1) link_MAN-ASN : angle 1.89805 ( 2) covalent geometry : bond 0.00740 (26366) covalent geometry : angle 0.68666 (35876) *********************** 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 132 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.1010 (ptt) cc_final: 0.0778 (ptt) REVERT: C 515 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8343 (p90) REVERT: A 340 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8428 (pp20) REVERT: A 346 ARG cc_start: 0.8464 (tmt170) cc_final: 0.8201 (tmt170) REVERT: A 790 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9133 (ptpp) REVERT: B 104 TRP cc_start: 0.7639 (m-90) cc_final: 0.7177 (m-90) REVERT: B 135 PHE cc_start: 0.8558 (m-80) cc_final: 0.8296 (m-80) REVERT: B 137 ASN cc_start: 0.8937 (m-40) cc_final: 0.8198 (p0) REVERT: B 571 ASP cc_start: 0.9067 (t0) cc_final: 0.8674 (t0) outliers start: 41 outliers final: 32 residues processed: 125 average time/residue: 0.3558 time to fit residues: 76.4720 Evaluate side-chains 122 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 2.843 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain C residue 242 LEU 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 1068 VAL 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 242 LEU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 311 optimal weight: 1.9990 chunk 319 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.112898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069313 restraints weight = 66601.361| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.92 r_work: 0.2860 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26440 Z= 0.122 Angle : 0.570 8.411 36055 Z= 0.291 Chirality : 0.045 0.289 4155 Planarity : 0.004 0.057 4605 Dihedral : 7.095 84.166 4136 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.17 % Allowed : 12.45 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3208 helix: 1.75 (0.21), residues: 656 sheet: 0.33 (0.20), residues: 612 loop : -1.86 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.002 0.000 HIS B1083 PHE 0.031 0.001 PHE A 392 TYR 0.031 0.001 TYR B 449 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 27) link_NAG-ASN : angle 2.52213 ( 81) link_ALPHA1-4 : bond 0.01359 ( 4) link_ALPHA1-4 : angle 2.10412 ( 12) hydrogen bonds : bond 0.06084 ( 984) hydrogen bonds : angle 4.93091 ( 2670) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.01418 ( 84) link_MAN-ASN : bond 0.00033 ( 1) link_MAN-ASN : angle 1.04585 ( 2) covalent geometry : bond 0.00262 (26366) covalent geometry : angle 0.55470 (35876) *********************** 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 134 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8468 (pp20) REVERT: A 365 TYR cc_start: 0.9330 (m-10) cc_final: 0.9080 (m-10) REVERT: B 104 TRP cc_start: 0.7654 (m-90) cc_final: 0.7249 (m-90) REVERT: B 135 PHE cc_start: 0.8508 (m-80) cc_final: 0.8298 (m-80) REVERT: B 137 ASN cc_start: 0.8953 (m-40) cc_final: 0.8149 (p0) REVERT: B 571 ASP cc_start: 0.9051 (t0) cc_final: 0.8631 (t0) REVERT: B 878 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8708 (mt) outliers start: 33 outliers final: 26 residues processed: 128 average time/residue: 0.3274 time to fit residues: 71.6351 Evaluate side-chains 125 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL 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 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE 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 242 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 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 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 150 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.112696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069160 restraints weight = 66419.157| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.90 r_work: 0.2854 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26440 Z= 0.134 Angle : 0.568 10.766 36055 Z= 0.290 Chirality : 0.045 0.289 4155 Planarity : 0.004 0.057 4605 Dihedral : 6.854 87.047 4136 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.34 % Allowed : 12.59 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3208 helix: 1.82 (0.21), residues: 663 sheet: 0.41 (0.20), residues: 601 loop : -1.80 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 PHE 0.018 0.001 PHE A 347 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 27) link_NAG-ASN : angle 2.48972 ( 81) link_ALPHA1-4 : bond 0.01405 ( 4) link_ALPHA1-4 : angle 1.87663 ( 12) hydrogen bonds : bond 0.06135 ( 984) hydrogen bonds : angle 4.86248 ( 2670) SS BOND : bond 0.00306 ( 42) SS BOND : angle 1.07798 ( 84) link_MAN-ASN : bond 0.00131 ( 1) link_MAN-ASN : angle 1.11754 ( 2) covalent geometry : bond 0.00305 (26366) covalent geometry : angle 0.55356 (35876) *********************** 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 137 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8500 (pp20) REVERT: A 346 ARG cc_start: 0.8477 (tmt170) cc_final: 0.8183 (tmt170) REVERT: A 365 TYR cc_start: 0.9350 (m-10) cc_final: 0.9081 (m-10) REVERT: A 387 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8693 (mt) REVERT: B 104 TRP cc_start: 0.7644 (m-90) cc_final: 0.7230 (m-90) REVERT: B 137 ASN cc_start: 0.8973 (m-40) cc_final: 0.8188 (p0) REVERT: B 571 ASP cc_start: 0.9050 (t0) cc_final: 0.8641 (t0) outliers start: 38 outliers final: 31 residues processed: 131 average time/residue: 0.3351 time to fit residues: 76.2712 Evaluate side-chains 127 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 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 C residue 1121 PHE 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 242 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 723 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 517 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 166 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.112501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069081 restraints weight = 66552.331| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.89 r_work: 0.2852 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26440 Z= 0.140 Angle : 0.564 8.407 36055 Z= 0.289 Chirality : 0.045 0.288 4155 Planarity : 0.004 0.057 4605 Dihedral : 6.715 86.216 4136 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.34 % Allowed : 12.84 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3208 helix: 1.86 (0.21), residues: 662 sheet: 0.39 (0.21), residues: 600 loop : -1.78 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 PHE 0.040 0.001 PHE A 392 TYR 0.023 0.001 TYR B 449 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 27) link_NAG-ASN : angle 2.45392 ( 81) link_ALPHA1-4 : bond 0.01245 ( 4) link_ALPHA1-4 : angle 1.86971 ( 12) hydrogen bonds : bond 0.06162 ( 984) hydrogen bonds : angle 4.83873 ( 2670) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.07024 ( 84) link_MAN-ASN : bond 0.00170 ( 1) link_MAN-ASN : angle 1.10545 ( 2) covalent geometry : bond 0.00323 (26366) covalent geometry : angle 0.54970 (35876) *********************** 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 135 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1017 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8617 (tt0) REVERT: A 340 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8505 (pp20) REVERT: A 346 ARG cc_start: 0.8427 (tmt170) cc_final: 0.8111 (tmt170) REVERT: A 365 TYR cc_start: 0.9345 (m-10) cc_final: 0.9042 (m-10) REVERT: A 387 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8727 (mt) REVERT: B 104 TRP cc_start: 0.7654 (m-90) cc_final: 0.7228 (m-90) REVERT: B 137 ASN cc_start: 0.9005 (m-40) cc_final: 0.8237 (p0) REVERT: B 571 ASP cc_start: 0.9044 (t0) cc_final: 0.8651 (t0) outliers start: 38 outliers final: 34 residues processed: 129 average time/residue: 0.4556 time to fit residues: 103.5351 Evaluate side-chains 130 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 3.596 ------------------------------------------------------------------------------- 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 C residue 1121 PHE 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 242 LEU 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 723 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 176 LEU 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 Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 301 optimal weight: 3.9990 chunk 196 optimal weight: 0.0010 chunk 291 optimal weight: 0.8980 chunk 205 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 233 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 277 optimal weight: 0.3980 overall best weight: 0.3944 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.114560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.071917 restraints weight = 66334.360| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.90 r_work: 0.2879 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26440 Z= 0.101 Angle : 0.539 8.596 36055 Z= 0.274 Chirality : 0.044 0.272 4155 Planarity : 0.004 0.058 4605 Dihedral : 6.133 76.156 4136 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.99 % Allowed : 13.44 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3208 helix: 2.06 (0.21), residues: 668 sheet: 0.37 (0.20), residues: 622 loop : -1.66 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.001 0.000 HIS B1083 PHE 0.036 0.001 PHE A 392 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 27) link_NAG-ASN : angle 2.25488 ( 81) link_ALPHA1-4 : bond 0.00989 ( 4) link_ALPHA1-4 : angle 2.06549 ( 12) hydrogen bonds : bond 0.04761 ( 984) hydrogen bonds : angle 4.61693 ( 2670) SS BOND : bond 0.00242 ( 42) SS BOND : angle 0.82304 ( 84) link_MAN-ASN : bond 0.00043 ( 1) link_MAN-ASN : angle 0.87328 ( 2) covalent geometry : bond 0.00209 (26366) covalent geometry : angle 0.52674 (35876) ********************** 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 134 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1017 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8544 (tt0) REVERT: A 340 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8492 (pp20) REVERT: A 346 ARG cc_start: 0.8438 (tmt170) cc_final: 0.8122 (tmt170) REVERT: A 365 TYR cc_start: 0.9354 (m-10) cc_final: 0.9054 (m-10) REVERT: A 387 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 453 TYR cc_start: 0.8830 (p90) cc_final: 0.8295 (p90) REVERT: A 786 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8416 (mmtm) REVERT: B 104 TRP cc_start: 0.7539 (m-90) cc_final: 0.7167 (m-90) REVERT: B 137 ASN cc_start: 0.9004 (m-40) cc_final: 0.8207 (p0) REVERT: B 571 ASP cc_start: 0.8975 (t0) cc_final: 0.8573 (t0) outliers start: 28 outliers final: 25 residues processed: 131 average time/residue: 0.3282 time to fit residues: 73.3775 Evaluate side-chains 119 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL 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 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 242 LEU 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 723 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 THR 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 Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 267 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 297 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 224 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063073 restraints weight = 64386.251| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.78 r_work: 0.2814 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26440 Z= 0.223 Angle : 0.630 9.734 36055 Z= 0.324 Chirality : 0.047 0.307 4155 Planarity : 0.004 0.057 4605 Dihedral : 6.492 80.216 4136 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.27 % Allowed : 13.37 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3208 helix: 1.71 (0.21), residues: 670 sheet: 0.20 (0.20), residues: 640 loop : -1.76 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.002 PHE A 392 TYR 0.022 0.001 TYR B 449 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 27) link_NAG-ASN : angle 2.55061 ( 81) link_ALPHA1-4 : bond 0.01074 ( 4) link_ALPHA1-4 : angle 1.90397 ( 12) hydrogen bonds : bond 0.07375 ( 984) hydrogen bonds : angle 4.99202 ( 2670) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.37704 ( 84) link_MAN-ASN : bond 0.00484 ( 1) link_MAN-ASN : angle 1.20768 ( 2) covalent geometry : bond 0.00544 (26366) covalent geometry : angle 0.61494 (35876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14764.86 seconds wall clock time: 255 minutes 52.85 seconds (15352.85 seconds total)