Starting phenix.real_space_refine on Wed Jun 18 12:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.map" model { file = "/net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usz_42524/06_2025/8usz_42524.cif" } resolution = 2.98 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= 0.016 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 95 5.16 5 C 13505 2.51 5 N 3511 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21179 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 6989 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 49, 'TRANS': 908} Chain breaks: 12 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 562 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 14, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 357 Chain: "B" Number of atoms: 6981 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 914, 6973 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 47, 'TRANS': 866} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 126 Conformer: "B" Number of residues, atoms: 914, 6973 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 47, 'TRANS': 866} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 126 bond proxies already assigned to first conformer: 7109 Chain: "C" Number of atoms: 6859 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 886, 6851 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 839} Chain breaks: 15 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Conformer: "B" Number of residues, atoms: 886, 6851 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 839} Chain breaks: 15 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 bond proxies already assigned to first conformer: 6990 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALEU B 753 " occ=0.53 ... (14 atoms not shown) pdb=" CD2BLEU B 753 " occ=0.47 residue: pdb=" N ALEU C 753 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU C 753 " occ=0.57 Time building chain proxies: 21.44, per 1000 atoms: 1.01 Number of scatterers: 21179 At special positions: 0 Unit cell: (137.25, 130.5, 179.25, 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 95 16.00 O 4068 8.00 N 3511 7.00 C 13505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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 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 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 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1401 " - " ASN A 331 " " NAG A1403 " - " ASN A 709 " " NAG A1404 " - " ASN A 717 " " NAG A1405 " - " ASN A 801 " " NAG A1406 " - " ASN A1074 " " NAG B2001 " - " ASN B 616 " " NAG B2002 " - " ASN B 709 " " NAG B2004 " - " ASN B 801 " " NAG C2004 " - " ASN C 801 " Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 4.2 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 22.9% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.221A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.893A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.603A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.764A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.557A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.380A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 937 removed outlier: 3.812A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.615A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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: 3.641A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1032 removed outlier: 3.626A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.255A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.033A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.647A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.585A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.659A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.576A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.569A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 939 Processing helix chain 'B' and resid 948 through 965 removed outlier: 3.729A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 977 through 982 Processing helix chain 'B' and resid 989 through 1032 removed outlier: 3.530A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.511A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.426A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.580A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.971A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.825A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.596A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.910A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 856' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.832A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.574A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.848A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.759A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 982 removed outlier: 3.682A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1033 removed outlier: 3.515A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.343A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.900A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.374A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.594A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.544A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 400 removed outlier: 3.679A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 584 through 586 removed outlier: 6.798A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.042A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 7.389A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.897A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.706A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 230 removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.508A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.561A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 357 removed outlier: 4.113A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.624A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 540 removed outlier: 5.564A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.819A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.345A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.547A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 224 through 230 removed outlier: 3.573A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.066A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 378 through 380 removed outlier: 3.919A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.583A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.315A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1076 through 1077 removed outlier: 3.661A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 698 hydrogen bonds defined for protein. 1902 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: 8.41 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3467 1.31 - 1.44: 5823 1.44 - 1.57: 12188 1.57 - 1.70: 2 1.70 - 1.82: 121 Bond restraints: 21601 Sorted by residual: bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" CA PHE C 817 " pdb=" C PHE C 817 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.24e-02 6.50e+03 2.66e+01 bond pdb=" N PHE C 817 " pdb=" CA PHE C 817 " ideal model delta sigma weight residual 1.459 1.400 0.059 1.17e-02 7.31e+03 2.55e+01 bond pdb=" CA GLN A 755 " pdb=" C GLN A 755 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.37e-02 5.33e+03 2.13e+01 bond pdb=" CA LYS A1045 " pdb=" CB LYS A1045 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.69e-02 3.50e+03 2.02e+01 ... (remaining 21596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 29224 3.50 - 6.99: 155 6.99 - 10.49: 24 10.49 - 13.99: 8 13.99 - 17.48: 4 Bond angle restraints: 29415 Sorted by residual: angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 94.52 17.48 1.40e+00 5.10e-01 1.56e+02 angle pdb=" CA PRO B 225 " pdb=" N PRO B 225 " pdb=" CD PRO B 225 " ideal model delta sigma weight residual 112.00 95.48 16.52 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA PRO B 987 " pdb=" N PRO B 987 " pdb=" CD PRO B 987 " ideal model delta sigma weight residual 112.00 103.51 8.49 1.40e+00 5.10e-01 3.68e+01 angle pdb=" N PRO C 987 " pdb=" CD PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 103.20 95.48 7.72 1.50e+00 4.44e-01 2.65e+01 angle pdb=" CB MET B 902 " pdb=" CG MET B 902 " pdb=" SD MET B 902 " ideal model delta sigma weight residual 112.70 127.38 -14.68 3.00e+00 1.11e-01 2.40e+01 ... (remaining 29410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 12057 21.19 - 42.38: 888 42.38 - 63.57: 183 63.57 - 84.77: 30 84.77 - 105.96: 34 Dihedral angle restraints: 13192 sinusoidal: 5178 harmonic: 8014 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 6.24 86.76 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.05 80.05 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -139.44 53.44 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 13189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3484 0.144 - 0.287: 26 0.287 - 0.431: 3 0.431 - 0.575: 0 0.575 - 0.718: 1 Chirality restraints: 3514 Sorted by residual: chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C2 NAG C2003 " pdb=" C1 NAG C2003 " pdb=" C3 NAG C2003 " pdb=" N2 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 3511 not shown) Planarity restraints: 3767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " 0.129 5.00e-02 4.00e+02 1.80e-01 5.16e+01 pdb=" N PRO B 225 " -0.310 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.126 5.00e-02 4.00e+02 1.73e-01 4.79e+01 pdb=" N PRO C 987 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.063 5.00e-02 4.00e+02 9.44e-02 1.42e+01 pdb=" N PRO A 987 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.053 5.00e-02 4.00e+02 ... (remaining 3764 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 99 2.53 - 3.13: 14104 3.13 - 3.72: 29825 3.72 - 4.31: 41570 4.31 - 4.90: 72182 Nonbonded interactions: 157780 Sorted by model distance: nonbonded pdb=" NE2 GLN A 895 " pdb=" O ALA C 706 " model vdw 1.942 3.120 nonbonded pdb=" CG1 VAL B 120 " pdb=" OD1 ASN B 122 " model vdw 2.003 3.460 nonbonded pdb=" OE1 GLN A 895 " pdb=" OG SER C 711 " model vdw 2.095 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.300 3.040 ... (remaining 157775 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 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 66 or resid 84 throug \ h 95 or resid 100 through 107 or resid 188 through 210 or resid 215 through 231 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 through 263 or resid 265 through 270 or (resid 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 331 or (resid 332 through 3 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 336 through \ 397 or (resid 398 through 403 and (name N or name CA or name C or name O or nam \ e CB )) or resid 404 through 440 or resid 492 or resid 498 or resid 510 through \ 518 or resid 521 through 528 or (resid 529 and (name N or name CA or name C or n \ ame O or name CB )) or resid 530 through 752 or resid 754 through 854 or (resid \ 855 and (name N or name CA or name C or name O or name CB )) or resid 856 throug \ h 1143 or resid 1401 through 1406)) selection = (chain 'B' and (resid 25 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 66 or resid 84 through 107 or (res \ id 188 through 189 and (name N or name CA or name C or name O or name CB )) or r \ esid 190 through 196 or resid 199 through 209 or (resid 210 through 215 and (nam \ e N or name CA or name C or name O or name CB )) or resid 216 through 332 or (re \ sid 333 through 335 and (name N or name CA or name C or name O or name CB )) or \ resid 336 or (resid 337 through 380 and (name N or name CA or name C or name O o \ r name CB )) or resid 381 or (resid 382 through 392 and (name N or name CA or na \ me C or name O or name CB )) or resid 393 through 395 or (resid 396 through 403 \ and (name N or name CA or name C or name O or name CB )) or (resid 404 through 4 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 413 or (res \ id 414 through 415 and (name N or name CA or name C or name O or name CB )) or r \ esid 416 or (resid 417 through 430 and (name N or name CA or name C or name O or \ name CB )) or resid 431 or (resid 432 through 440 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 461 and (name N or name CA or name C or na \ me O or name CB )) or (resid 466 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 510 and (name N or name CA or name C or name O or name CB )) \ or resid 511 through 514 or (resid 515 through 518 and (name N or name CA or na \ me C or name O or name CB )) or (resid 521 through 522 and (name N or name CA or \ name C or name O or name CB )) or resid 523 or (resid 524 and (name N or name C \ A or name C or name O or name CB )) or resid 525 through 543 or (resid 544 and ( \ name N or name CA or name C or name O or name CB )) or resid 545 through 675 or \ resid 689 through 752 or resid 754 through 938 or resid 946 through 1143 or resi \ d 2001 through 2006)) selection = (chain 'C' and (resid 25 through 107 or (resid 188 through 189 and (name N or na \ me CA or name C or name O or name CB )) or resid 190 through 209 or (resid 210 a \ nd (name N or name CA or name C or name O or name CB )) or resid 215 through 263 \ or resid 265 through 270 or (resid 271 and (name N or name CA or name C or name \ O or name CB )) or resid 272 through 331 or (resid 332 through 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 or (resid 337 through \ 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or (re \ sid 382 through 392 and (name N or name CA or name C or name O or name CB )) or \ resid 393 through 395 or (resid 396 through 403 and (name N or name CA or name C \ or name O or name CB )) or resid 404 or (resid 405 through 412 and (name N or n \ ame CA or name C or name O or name CB )) or resid 413 or (resid 414 through 415 \ and (name N or name CA or name C or name O or name CB )) or resid 416 or (resid \ 417 through 430 and (name N or name CA or name C or name O or name CB )) or resi \ d 431 or (resid 432 through 440 and (name N or name CA or name C or name O or na \ me CB )) or (resid 461 and (name N or name CA or name C or name O or name CB )) \ or (resid 466 and (name N or name CA or name C or name O or name CB )) or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throu \ gh 514 or (resid 515 through 522 and (name N or name CA or name C or name O or n \ ame CB )) or resid 523 or (resid 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 through 528 or (resid 529 and (name N or name CA or n \ ame C or name O or name CB )) or resid 530 through 543 or (resid 544 and (name N \ or name CA or name C or name O or name CB )) or resid 545 through 675 or resid \ 689 through 752 or resid 754 through 854 or (resid 855 and (name N or name CA or \ name C or name O or name CB )) or resid 856 through 938 or resid 946 through 11 \ 43 or resid 2001 through 2006)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.43 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: 12.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 61.390 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 21640 Z= 0.231 Angle : 0.793 17.482 29505 Z= 0.405 Chirality : 0.052 0.718 3514 Planarity : 0.007 0.180 3758 Dihedral : 16.217 105.957 7917 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.90 % Allowed : 19.25 % Favored : 78.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2676 helix: -0.97 (0.19), residues: 548 sheet: -0.73 (0.23), residues: 512 loop : -2.01 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 PHE 0.030 0.001 PHE B 823 TYR 0.036 0.001 TYR C 380 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.01089 ( 9) link_NAG-ASN : angle 3.44087 ( 27) link_BETA1-4 : bond 0.01822 ( 3) link_BETA1-4 : angle 7.68291 ( 9) hydrogen bonds : bond 0.20746 ( 686) hydrogen bonds : angle 8.24766 ( 1902) SS BOND : bond 0.00176 ( 27) SS BOND : angle 0.70114 ( 54) covalent geometry : bond 0.00443 (21601) covalent geometry : angle 0.77514 (29415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: B 177 MET cc_start: 0.5699 (mmt) cc_final: 0.4678 (pp-130) REVERT: C 380 TYR cc_start: 0.6893 (m-80) cc_final: 0.6518 (m-80) outliers start: 42 outliers final: 27 residues processed: 252 average time/residue: 0.9686 time to fit residues: 292.4532 Evaluate side-chains 182 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 214 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN A 895 GLN A 935 GLN A1048 HIS B 52 GLN B 710 ASN C 360 ASN C 394 ASN C 613 GLN C 762 GLN C 901 GLN C1002 GLN C1005 GLN C1134 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.178245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140540 restraints weight = 28956.154| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.28 r_work: 0.3461 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21640 Z= 0.129 Angle : 0.588 11.286 29505 Z= 0.289 Chirality : 0.045 0.352 3514 Planarity : 0.005 0.108 3758 Dihedral : 9.784 93.596 3461 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.89 % Allowed : 20.47 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.15), residues: 2676 helix: 0.16 (0.21), residues: 565 sheet: -0.34 (0.23), residues: 519 loop : -1.94 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 886 HIS 0.005 0.001 HIS A1048 PHE 0.018 0.001 PHE B 823 TYR 0.025 0.001 TYR B1067 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 9) link_NAG-ASN : angle 2.29813 ( 27) link_BETA1-4 : bond 0.01020 ( 3) link_BETA1-4 : angle 4.41997 ( 9) hydrogen bonds : bond 0.03972 ( 686) hydrogen bonds : angle 5.73320 ( 1902) SS BOND : bond 0.00172 ( 27) SS BOND : angle 0.72169 ( 54) covalent geometry : bond 0.00310 (21601) covalent geometry : angle 0.57853 (29415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6532 (mtp-110) cc_final: 0.6169 (mtt-85) REVERT: A 935 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: A 1002 GLN cc_start: 0.8076 (mp10) cc_final: 0.7791 (mp-120) REVERT: B 177 MET cc_start: 0.6296 (mmt) cc_final: 0.5677 (pp-130) REVERT: B 203 ILE cc_start: 0.7463 (mt) cc_final: 0.7096 (mp) REVERT: B 851 CYS cc_start: 0.1409 (OUTLIER) cc_final: 0.1087 (p) REVERT: B 1111 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: C 265 TYR cc_start: 0.7214 (p90) cc_final: 0.6939 (p90) REVERT: C 394 ASN cc_start: 0.8008 (t0) cc_final: 0.7806 (t0) REVERT: C 554 GLU cc_start: 0.7449 (pt0) cc_final: 0.6811 (pp20) outliers start: 64 outliers final: 26 residues processed: 223 average time/residue: 0.9296 time to fit residues: 250.5962 Evaluate side-chains 179 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 169 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 242 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 762 GLN A 935 GLN A1048 HIS B 52 GLN B 370 ASN B 710 ASN C 360 ASN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125691 restraints weight = 28845.278| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.21 r_work: 0.3450 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21640 Z= 0.186 Angle : 0.638 11.111 29505 Z= 0.313 Chirality : 0.048 0.419 3514 Planarity : 0.005 0.088 3758 Dihedral : 8.142 90.119 3429 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.98 % Allowed : 19.39 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.66 (0.15), residues: 2676 helix: 0.32 (0.22), residues: 570 sheet: -0.55 (0.22), residues: 532 loop : -1.93 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 886 HIS 0.007 0.001 HIS B1048 PHE 0.022 0.002 PHE B 392 TYR 0.023 0.002 TYR B1067 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 9) link_NAG-ASN : angle 2.60239 ( 27) link_BETA1-4 : bond 0.01037 ( 3) link_BETA1-4 : angle 4.64650 ( 9) hydrogen bonds : bond 0.04579 ( 686) hydrogen bonds : angle 5.51578 ( 1902) SS BOND : bond 0.00334 ( 27) SS BOND : angle 1.04384 ( 54) covalent geometry : bond 0.00453 (21601) covalent geometry : angle 0.62748 (29415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 154 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: A 543 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: A 1002 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: B 177 MET cc_start: 0.6451 (mmt) cc_final: 0.5846 (pp-130) REVERT: B 203 ILE cc_start: 0.7548 (mt) cc_final: 0.7207 (mp) REVERT: B 239 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: B 851 CYS cc_start: 0.1683 (OUTLIER) cc_final: 0.1436 (p) REVERT: B 1111 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: C 265 TYR cc_start: 0.7401 (p90) cc_final: 0.7166 (p90) REVERT: C 554 GLU cc_start: 0.7526 (pt0) cc_final: 0.6813 (pp20) REVERT: C 693 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7820 (pp) REVERT: C 787 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7894 (mm-40) outliers start: 88 outliers final: 46 residues processed: 228 average time/residue: 0.9649 time to fit residues: 269.0487 Evaluate side-chains 195 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 265 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 50.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1048 HIS B 49 HIS B 52 GLN B 710 ASN B 751 ASN C 360 ASN C 935 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.174600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136751 restraints weight = 29211.886| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.35 r_work: 0.3387 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21640 Z= 0.135 Angle : 0.576 11.095 29505 Z= 0.281 Chirality : 0.045 0.430 3514 Planarity : 0.004 0.077 3758 Dihedral : 7.164 87.987 3423 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.12 % Allowed : 20.29 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2676 helix: 0.65 (0.22), residues: 566 sheet: -0.49 (0.23), residues: 525 loop : -1.86 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 886 HIS 0.004 0.001 HIS B1101 PHE 0.014 0.001 PHE A1121 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 2.52423 ( 27) link_BETA1-4 : bond 0.01154 ( 3) link_BETA1-4 : angle 4.43347 ( 9) hydrogen bonds : bond 0.03779 ( 686) hydrogen bonds : angle 5.25151 ( 1902) SS BOND : bond 0.00267 ( 27) SS BOND : angle 0.86920 ( 54) covalent geometry : bond 0.00322 (21601) covalent geometry : angle 0.56579 (29415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 155 time to evaluate : 2.252 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: A 1123 SER cc_start: 0.8291 (t) cc_final: 0.8025 (p) REVERT: B 177 MET cc_start: 0.6522 (mmt) cc_final: 0.6013 (pp-130) REVERT: B 203 ILE cc_start: 0.7366 (mt) cc_final: 0.6999 (mp) REVERT: B 239 GLN cc_start: 0.6076 (OUTLIER) cc_final: 0.5864 (mp10) REVERT: B 1111 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: C 265 TYR cc_start: 0.7367 (p90) cc_final: 0.7106 (p90) REVERT: C 554 GLU cc_start: 0.7560 (pt0) cc_final: 0.6856 (pp20) REVERT: C 693 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7627 (pp) REVERT: C 787 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7811 (mm-40) outliers start: 69 outliers final: 39 residues processed: 216 average time/residue: 0.8446 time to fit residues: 222.4840 Evaluate side-chains 188 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 52 GLN B 710 ASN C 360 ASN C 935 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.173294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123756 restraints weight = 29116.392| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.26 r_work: 0.3408 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21640 Z= 0.160 Angle : 0.600 11.017 29505 Z= 0.293 Chirality : 0.046 0.492 3514 Planarity : 0.004 0.072 3758 Dihedral : 6.881 85.021 3423 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.71 % Allowed : 19.93 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2676 helix: 0.73 (0.22), residues: 564 sheet: -0.64 (0.22), residues: 560 loop : -1.81 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 PHE 0.016 0.001 PHE B1089 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 9) link_NAG-ASN : angle 2.73908 ( 27) link_BETA1-4 : bond 0.01150 ( 3) link_BETA1-4 : angle 4.45712 ( 9) hydrogen bonds : bond 0.04042 ( 686) hydrogen bonds : angle 5.20302 ( 1902) SS BOND : bond 0.00310 ( 27) SS BOND : angle 0.90450 ( 54) covalent geometry : bond 0.00391 (21601) covalent geometry : angle 0.58856 (29415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 150 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 1123 SER cc_start: 0.8357 (t) cc_final: 0.8126 (p) REVERT: B 177 MET cc_start: 0.6677 (mmt) cc_final: 0.6157 (pp-130) REVERT: B 203 ILE cc_start: 0.7466 (mt) cc_final: 0.7095 (mp) REVERT: B 239 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: B 1111 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: C 265 TYR cc_start: 0.7462 (p90) cc_final: 0.7200 (p90) REVERT: C 554 GLU cc_start: 0.7686 (pt0) cc_final: 0.6923 (pp20) REVERT: C 693 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (pp) REVERT: C 787 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7919 (mm-40) outliers start: 82 outliers final: 54 residues processed: 215 average time/residue: 0.9023 time to fit residues: 236.2821 Evaluate side-chains 201 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 8 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 935 GLN A1048 HIS B 52 GLN B 710 ASN C 52 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123421 restraints weight = 29004.502| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.28 r_work: 0.3402 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21640 Z= 0.208 Angle : 0.654 11.552 29505 Z= 0.322 Chirality : 0.048 0.501 3514 Planarity : 0.005 0.068 3758 Dihedral : 7.005 82.637 3423 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.25 % Allowed : 19.57 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2676 helix: 0.54 (0.22), residues: 563 sheet: -0.68 (0.22), residues: 547 loop : -1.87 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.007 0.001 HIS B1048 PHE 0.020 0.002 PHE B1089 TYR 0.021 0.002 TYR B1067 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 9) link_NAG-ASN : angle 3.00703 ( 27) link_BETA1-4 : bond 0.01083 ( 3) link_BETA1-4 : angle 4.46837 ( 9) hydrogen bonds : bond 0.04538 ( 686) hydrogen bonds : angle 5.42342 ( 1902) SS BOND : bond 0.00394 ( 27) SS BOND : angle 1.08925 ( 54) covalent geometry : bond 0.00511 (21601) covalent geometry : angle 0.64220 (29415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 144 time to evaluate : 2.492 Fit side-chains REVERT: A 1123 SER cc_start: 0.8369 (t) cc_final: 0.8149 (p) REVERT: B 203 ILE cc_start: 0.7501 (mt) cc_final: 0.7157 (mp) REVERT: B 1111 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: C 265 TYR cc_start: 0.7499 (p90) cc_final: 0.7299 (p90) REVERT: C 554 GLU cc_start: 0.7735 (pt0) cc_final: 0.6963 (pp20) REVERT: C 693 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 787 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7851 (mm-40) outliers start: 94 outliers final: 58 residues processed: 220 average time/residue: 0.9035 time to fit residues: 241.1227 Evaluate side-chains 200 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 193 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 66 optimal weight: 0.0870 chunk 68 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 762 GLN A 804 GLN A1048 HIS B 52 GLN B 66 HIS B 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137317 restraints weight = 28846.233| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.03 r_work: 0.3394 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21640 Z= 0.104 Angle : 0.558 10.973 29505 Z= 0.273 Chirality : 0.045 0.492 3514 Planarity : 0.004 0.066 3758 Dihedral : 6.492 81.505 3423 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.35 % Allowed : 22.01 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.32 (0.16), residues: 2676 helix: 0.99 (0.23), residues: 558 sheet: -0.59 (0.23), residues: 532 loop : -1.74 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.003 0.001 HIS B1101 PHE 0.015 0.001 PHE A1121 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 9) link_NAG-ASN : angle 2.83395 ( 27) link_BETA1-4 : bond 0.01144 ( 3) link_BETA1-4 : angle 4.35711 ( 9) hydrogen bonds : bond 0.03416 ( 686) hydrogen bonds : angle 5.04033 ( 1902) SS BOND : bond 0.00197 ( 27) SS BOND : angle 0.74215 ( 54) covalent geometry : bond 0.00240 (21601) covalent geometry : angle 0.54608 (29415) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.6127 (m) cc_final: 0.5765 (p) REVERT: A 549 THR cc_start: 0.8189 (m) cc_final: 0.7955 (p) REVERT: B 177 MET cc_start: 0.6678 (mmp) cc_final: 0.6047 (pp-130) REVERT: B 203 ILE cc_start: 0.7337 (mt) cc_final: 0.6976 (mp) REVERT: B 1111 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: C 265 TYR cc_start: 0.7348 (p90) cc_final: 0.7107 (p90) REVERT: C 323 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8228 (t) REVERT: C 554 GLU cc_start: 0.7600 (pt0) cc_final: 0.6896 (pp20) REVERT: C 693 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7604 (pp) REVERT: C 787 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7777 (mm-40) outliers start: 52 outliers final: 29 residues processed: 195 average time/residue: 0.9757 time to fit residues: 230.4832 Evaluate side-chains 175 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 12 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 935 GLN B 52 GLN B 710 ASN B1142 GLN C 52 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121860 restraints weight = 29079.090| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.20 r_work: 0.3409 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21640 Z= 0.200 Angle : 0.641 10.988 29505 Z= 0.315 Chirality : 0.048 0.524 3514 Planarity : 0.005 0.064 3758 Dihedral : 6.755 79.798 3422 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.07 % Allowed : 21.10 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2676 helix: 0.71 (0.22), residues: 566 sheet: -0.46 (0.23), residues: 510 loop : -1.80 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 886 HIS 0.006 0.001 HIS B1048 PHE 0.019 0.002 PHE B1089 TYR 0.020 0.002 TYR B1067 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 9) link_NAG-ASN : angle 3.11858 ( 27) link_BETA1-4 : bond 0.01126 ( 3) link_BETA1-4 : angle 4.44140 ( 9) hydrogen bonds : bond 0.04337 ( 686) hydrogen bonds : angle 5.25300 ( 1902) SS BOND : bond 0.00347 ( 27) SS BOND : angle 1.02953 ( 54) covalent geometry : bond 0.00491 (21601) covalent geometry : angle 0.62818 (29415) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 4.276 Fit side-chains REVERT: A 131 CYS cc_start: 0.6326 (m) cc_final: 0.5969 (p) REVERT: B 177 MET cc_start: 0.6666 (mmp) cc_final: 0.6000 (pp-130) REVERT: B 203 ILE cc_start: 0.7472 (mt) cc_final: 0.7123 (mp) REVERT: B 1111 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: C 265 TYR cc_start: 0.7447 (p90) cc_final: 0.7197 (p90) REVERT: C 323 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 554 GLU cc_start: 0.7698 (pt0) cc_final: 0.6907 (pp20) REVERT: C 693 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (pt) REVERT: C 787 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7822 (mm-40) outliers start: 68 outliers final: 46 residues processed: 203 average time/residue: 1.1014 time to fit residues: 271.5496 Evaluate side-chains 190 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 14 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 267 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 155 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 935 GLN B 52 GLN B 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134936 restraints weight = 28999.474| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.10 r_work: 0.3381 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21640 Z= 0.147 Angle : 0.596 10.959 29505 Z= 0.292 Chirality : 0.047 0.570 3514 Planarity : 0.004 0.064 3758 Dihedral : 6.580 79.049 3422 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.76 % Allowed : 21.51 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2676 helix: 0.85 (0.22), residues: 560 sheet: -0.40 (0.24), residues: 479 loop : -1.78 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.017 0.001 PHE A1121 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 9) link_NAG-ASN : angle 3.10174 ( 27) link_BETA1-4 : bond 0.01152 ( 3) link_BETA1-4 : angle 4.36981 ( 9) hydrogen bonds : bond 0.03838 ( 686) hydrogen bonds : angle 5.13608 ( 1902) SS BOND : bond 0.00265 ( 27) SS BOND : angle 0.87671 ( 54) covalent geometry : bond 0.00356 (21601) covalent geometry : angle 0.58348 (29415) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 2.212 Fit side-chains REVERT: A 131 CYS cc_start: 0.6302 (m) cc_final: 0.5926 (p) REVERT: B 177 MET cc_start: 0.6580 (mmp) cc_final: 0.6028 (pp-130) REVERT: B 203 ILE cc_start: 0.7367 (mt) cc_final: 0.7007 (mp) REVERT: B 1111 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: C 265 TYR cc_start: 0.7413 (p90) cc_final: 0.7164 (p90) REVERT: C 323 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 554 GLU cc_start: 0.7607 (pt0) cc_final: 0.6914 (pp20) REVERT: C 693 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (pp) REVERT: C 787 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7753 (mm-40) outliers start: 61 outliers final: 46 residues processed: 192 average time/residue: 0.9013 time to fit residues: 209.9360 Evaluate side-chains 190 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 239 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 271 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 935 GLN B 52 GLN B 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136587 restraints weight = 28967.976| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.08 r_work: 0.3399 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21640 Z= 0.110 Angle : 0.566 10.994 29505 Z= 0.276 Chirality : 0.045 0.581 3514 Planarity : 0.004 0.064 3758 Dihedral : 6.341 77.761 3422 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.30 % Allowed : 22.10 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2676 helix: 1.09 (0.23), residues: 558 sheet: -0.28 (0.23), residues: 492 loop : -1.73 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 PHE 0.016 0.001 PHE A1121 TYR 0.020 0.001 TYR C1138 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 9) link_NAG-ASN : angle 3.20477 ( 27) link_BETA1-4 : bond 0.01187 ( 3) link_BETA1-4 : angle 4.31773 ( 9) hydrogen bonds : bond 0.03404 ( 686) hydrogen bonds : angle 4.94644 ( 1902) SS BOND : bond 0.00197 ( 27) SS BOND : angle 0.77732 ( 54) covalent geometry : bond 0.00261 (21601) covalent geometry : angle 0.55238 (29415) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 3.014 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.6293 (m) cc_final: 0.5964 (p) REVERT: B 177 MET cc_start: 0.6562 (mmp) cc_final: 0.5965 (pp-130) REVERT: B 203 ILE cc_start: 0.7365 (mt) cc_final: 0.7002 (mp) REVERT: B 1111 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: C 265 TYR cc_start: 0.7350 (p90) cc_final: 0.7114 (p90) REVERT: C 323 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8331 (t) REVERT: C 554 GLU cc_start: 0.7560 (pt0) cc_final: 0.6877 (pp20) REVERT: C 693 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7615 (pp) REVERT: C 787 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7730 (mm-40) outliers start: 51 outliers final: 36 residues processed: 186 average time/residue: 1.1457 time to fit residues: 262.7090 Evaluate side-chains 177 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 259 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 chunk 254 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 52 GLN B 196 ASN B 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121986 restraints weight = 29220.113| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.10 r_work: 0.3441 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21640 Z= 0.139 Angle : 0.587 10.964 29505 Z= 0.287 Chirality : 0.046 0.549 3514 Planarity : 0.004 0.064 3758 Dihedral : 6.364 76.228 3422 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.49 % Allowed : 22.19 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2676 helix: 0.97 (0.22), residues: 567 sheet: -0.38 (0.23), residues: 502 loop : -1.68 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS B1048 PHE 0.017 0.001 PHE A1121 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 9) link_NAG-ASN : angle 3.42683 ( 27) link_BETA1-4 : bond 0.01165 ( 3) link_BETA1-4 : angle 4.30933 ( 9) hydrogen bonds : bond 0.03687 ( 686) hydrogen bonds : angle 4.98314 ( 1902) SS BOND : bond 0.00259 ( 27) SS BOND : angle 0.84929 ( 54) covalent geometry : bond 0.00336 (21601) covalent geometry : angle 0.57300 (29415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16848.86 seconds wall clock time: 291 minutes 21.89 seconds (17481.89 seconds total)