Starting phenix.real_space_refine on Sun Oct 12 04:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usz_42524/10_2025/8usz_42524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usz_42524/10_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_42524/10_2025/8usz_42524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usz_42524/10_2025/8usz_42524.map" model { file = "/net/cci-nas-00/data/ceres_data/8usz_42524/10_2025/8usz_42524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usz_42524/10_2025/8usz_42524.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'PHE:plan': 14, 'TYR:plan': 13, 'ASN:plan1': 17, 'GLN:plan1': 5, 'GLU:plan': 6, 'ASP:plan': 8, 'HIS:plan': 3, 'TRP:plan': 2, 'ARG:plan': 6} 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: {'PHE:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS: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: {'PHE:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS: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: {'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5} 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: {'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5} 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: 7.52, per 1000 atoms: 0.36 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: 1.55 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 0.0 nanoseconds 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: 0.84 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: 3.90 Time building geometry restraints manager: 2.11 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 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 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 20 \ 06)) } 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: 14.130 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- 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 : 3.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 567 TYR 0.036 0.001 TYR C 380 PHE 0.030 0.001 PHE B 823 TRP 0.018 0.001 TRP B 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00443 (21601) covalent geometry : angle 0.77514 (29415) SS BOND : bond 0.00176 ( 27) SS BOND : angle 0.70114 ( 54) hydrogen bonds : bond 0.20746 ( 686) hydrogen bonds : angle 8.24766 ( 1902) link_BETA1-4 : bond 0.01822 ( 3) link_BETA1-4 : angle 7.68291 ( 9) link_NAG-ASN : bond 0.01089 ( 9) link_NAG-ASN : angle 3.44087 ( 27) *********************** 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 : 0.768 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: 0.4241 time to fit residues: 126.8935 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 : 0.777 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.0370 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 196 ASN B 710 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 = 0.4247 r_free = 0.4247 target = 0.178113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140046 restraints weight = 28992.364| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 4.22 r_work: 0.3460 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21640 Z= 0.131 Angle : 0.591 11.390 29505 Z= 0.290 Chirality : 0.046 0.377 3514 Planarity : 0.006 0.113 3758 Dihedral : 9.836 93.683 3461 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.94 % Allowed : 20.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 2676 helix: 0.14 (0.21), residues: 564 sheet: -0.34 (0.23), residues: 519 loop : -1.95 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.026 0.001 TYR B1067 PHE 0.017 0.001 PHE B 823 TRP 0.021 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00314 (21601) covalent geometry : angle 0.58121 (29415) SS BOND : bond 0.00180 ( 27) SS BOND : angle 0.73147 ( 54) hydrogen bonds : bond 0.04168 ( 686) hydrogen bonds : angle 5.77015 ( 1902) link_BETA1-4 : bond 0.01179 ( 3) link_BETA1-4 : angle 4.46310 ( 9) link_NAG-ASN : bond 0.00619 ( 9) link_NAG-ASN : angle 2.38386 ( 27) *********************** 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 235 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6541 (mtp-110) cc_final: 0.6166 (mtt-85) REVERT: A 935 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: A 1002 GLN cc_start: 0.8077 (mp10) cc_final: 0.7788 (mp-120) REVERT: B 177 MET cc_start: 0.6277 (mmt) cc_final: 0.5669 (pp-130) REVERT: B 203 ILE cc_start: 0.7458 (mt) cc_final: 0.7113 (mp) REVERT: B 851 CYS cc_start: 0.1404 (OUTLIER) cc_final: 0.1084 (p) REVERT: B 1111 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: C 265 TYR cc_start: 0.7217 (p90) cc_final: 0.6898 (p90) REVERT: C 394 ASN cc_start: 0.8017 (t0) cc_final: 0.7805 (t0) REVERT: C 554 GLU cc_start: 0.7427 (pt0) cc_final: 0.6798 (pp20) outliers start: 65 outliers final: 26 residues processed: 225 average time/residue: 0.4081 time to fit residues: 110.7634 Evaluate side-chains 177 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 221 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 B 49 HIS B 52 GLN B 370 ASN B 710 ASN C 965 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140166 restraints weight = 29063.922| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 4.10 r_work: 0.3474 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21640 Z= 0.112 Angle : 0.555 11.150 29505 Z= 0.269 Chirality : 0.045 0.415 3514 Planarity : 0.005 0.089 3758 Dihedral : 8.004 91.257 3429 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.98 % Allowed : 20.24 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.16), residues: 2676 helix: 0.68 (0.22), residues: 565 sheet: -0.38 (0.23), residues: 503 loop : -1.82 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.021 0.001 TYR B1067 PHE 0.028 0.001 PHE B 392 TRP 0.018 0.001 TRP B 886 HIS 0.008 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00263 (21601) covalent geometry : angle 0.54486 (29415) SS BOND : bond 0.00236 ( 27) SS BOND : angle 0.68325 ( 54) hydrogen bonds : bond 0.03694 ( 686) hydrogen bonds : angle 5.31736 ( 1902) link_BETA1-4 : bond 0.01193 ( 3) link_BETA1-4 : angle 4.53020 ( 9) link_NAG-ASN : bond 0.00577 ( 9) link_NAG-ASN : angle 2.38474 ( 27) *********************** 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 222 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7923 (mp-120) REVERT: B 177 MET cc_start: 0.6338 (mmt) cc_final: 0.5745 (pp-130) REVERT: B 203 ILE cc_start: 0.7414 (mt) cc_final: 0.7062 (mp) REVERT: B 239 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: B 1111 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: C 265 TYR cc_start: 0.7200 (p90) cc_final: 0.6878 (p90) REVERT: C 394 ASN cc_start: 0.7943 (t0) cc_final: 0.7730 (t0) REVERT: C 554 GLU cc_start: 0.7403 (pt0) cc_final: 0.6779 (pp20) REVERT: C 693 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7654 (pp) REVERT: C 787 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7796 (mm-40) outliers start: 66 outliers final: 26 residues processed: 212 average time/residue: 0.4008 time to fit residues: 102.3916 Evaluate side-chains 178 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 641 ASN 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 383 SER 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 606 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1111 GLU 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 620 VAL Chi-restraints excluded: chain C residue 693 ILE 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 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE 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 256 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 709 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.171819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121544 restraints weight = 29150.242| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.20 r_work: 0.3420 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 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 = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21640 Z= 0.240 Angle : 0.688 11.724 29505 Z= 0.339 Chirality : 0.050 0.552 3514 Planarity : 0.005 0.079 3758 Dihedral : 7.605 87.614 3425 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.07 % Allowed : 19.43 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 2676 helix: 0.26 (0.21), residues: 574 sheet: -0.55 (0.22), residues: 549 loop : -1.95 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 319 TYR 0.022 0.002 TYR B1067 PHE 0.023 0.002 PHE B1089 TRP 0.025 0.002 TRP B 886 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00590 (21601) covalent geometry : angle 0.67695 (29415) SS BOND : bond 0.00410 ( 27) SS BOND : angle 1.17664 ( 54) hydrogen bonds : bond 0.04939 ( 686) hydrogen bonds : angle 5.57001 ( 1902) link_BETA1-4 : bond 0.01060 ( 3) link_BETA1-4 : angle 4.53670 ( 9) link_NAG-ASN : bond 0.00926 ( 9) link_NAG-ASN : angle 2.82372 ( 27) *********************** 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 240 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 150 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 543 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: A 935 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: A 1002 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: A 1050 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: A 1123 SER cc_start: 0.8393 (t) cc_final: 0.8143 (p) REVERT: B 177 MET cc_start: 0.6547 (mmt) cc_final: 0.6017 (pp-130) REVERT: B 203 ILE cc_start: 0.7574 (mt) cc_final: 0.7189 (mp) REVERT: B 239 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5946 (mp10) REVERT: B 1111 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: C 265 TYR cc_start: 0.7511 (p90) cc_final: 0.7278 (p90) REVERT: C 394 ASN cc_start: 0.8030 (t0) cc_final: 0.7823 (t0) REVERT: C 554 GLU cc_start: 0.7637 (pt0) cc_final: 0.6892 (pp20) REVERT: C 693 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (pt) REVERT: C 787 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7866 (mm-40) outliers start: 90 outliers final: 51 residues processed: 224 average time/residue: 0.3915 time to fit residues: 105.7776 Evaluate side-chains 199 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 140 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL 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 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET 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 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 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 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 977 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 243 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 50.0000 chunk 15 optimal weight: 0.0370 chunk 165 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 162 optimal weight: 0.0470 chunk 121 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 263 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 B 52 GLN B 710 ASN C 360 ASN C 709 ASN C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137340 restraints weight = 28775.785| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.02 r_work: 0.3428 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21640 Z= 0.096 Angle : 0.543 11.035 29505 Z= 0.263 Chirality : 0.044 0.448 3514 Planarity : 0.004 0.073 3758 Dihedral : 6.728 86.309 3423 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.21 % Allowed : 21.37 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.16), residues: 2676 helix: 0.87 (0.22), residues: 567 sheet: -0.45 (0.23), residues: 531 loop : -1.78 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.013 0.001 PHE A1121 TRP 0.015 0.001 TRP B 886 HIS 0.002 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00217 (21601) covalent geometry : angle 0.53143 (29415) SS BOND : bond 0.00175 ( 27) SS BOND : angle 0.71123 ( 54) hydrogen bonds : bond 0.03347 ( 686) hydrogen bonds : angle 5.04770 ( 1902) link_BETA1-4 : bond 0.01129 ( 3) link_BETA1-4 : angle 4.36977 ( 9) link_NAG-ASN : bond 0.00636 ( 9) link_NAG-ASN : angle 2.70068 ( 27) *********************** 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 200 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 1123 SER cc_start: 0.8181 (t) cc_final: 0.7951 (p) REVERT: B 177 MET cc_start: 0.6564 (mmt) cc_final: 0.6017 (pp-130) REVERT: B 203 ILE cc_start: 0.7448 (mt) cc_final: 0.7098 (mp) REVERT: B 239 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5991 (mp10) REVERT: C 265 TYR cc_start: 0.7354 (p90) cc_final: 0.7111 (p90) REVERT: C 554 GLU cc_start: 0.7521 (pt0) cc_final: 0.6866 (pp20) REVERT: C 693 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7588 (pp) REVERT: C 787 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7755 (mm-40) outliers start: 49 outliers final: 26 residues processed: 189 average time/residue: 0.4324 time to fit residues: 97.8713 Evaluate side-chains 171 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 704 SER 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 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 531 THR Chi-restraints excluded: chain B residue 606 ASN 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 C residue 41 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL 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 1129 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 246 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 B 751 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.174225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135448 restraints weight = 28828.901| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.91 r_work: 0.3374 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 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 = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21640 Z= 0.138 Angle : 0.571 10.993 29505 Z= 0.279 Chirality : 0.046 0.440 3514 Planarity : 0.004 0.070 3758 Dihedral : 6.632 84.203 3422 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.58 % Allowed : 20.88 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.16), residues: 2676 helix: 0.86 (0.22), residues: 573 sheet: -0.51 (0.22), residues: 545 loop : -1.72 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.021 0.001 TYR B1067 PHE 0.014 0.001 PHE A1121 TRP 0.015 0.001 TRP B 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00334 (21601) covalent geometry : angle 0.55977 (29415) SS BOND : bond 0.00247 ( 27) SS BOND : angle 0.84274 ( 54) hydrogen bonds : bond 0.03709 ( 686) hydrogen bonds : angle 5.04914 ( 1902) link_BETA1-4 : bond 0.01179 ( 3) link_BETA1-4 : angle 4.39301 ( 9) link_NAG-ASN : bond 0.00674 ( 9) link_NAG-ASN : angle 2.71972 ( 27) *********************** 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 203 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 1123 SER cc_start: 0.8259 (t) cc_final: 0.8041 (p) REVERT: B 177 MET cc_start: 0.6674 (mmt) cc_final: 0.6143 (pp-130) REVERT: B 203 ILE cc_start: 0.7415 (mt) cc_final: 0.7041 (mp) REVERT: B 239 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5942 (mp10) REVERT: B 1111 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: C 265 TYR cc_start: 0.7382 (p90) cc_final: 0.7107 (p90) REVERT: C 554 GLU cc_start: 0.7604 (pt0) cc_final: 0.6886 (pp20) REVERT: C 693 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7674 (pp) REVERT: C 787 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7771 (mm-40) outliers start: 57 outliers final: 39 residues processed: 192 average time/residue: 0.3827 time to fit residues: 89.6390 Evaluate side-chains 182 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 530 SER Chi-restraints excluded: chain A residue 534 VAL 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 994 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 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 606 ASN 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 1111 GLU Chi-restraints excluded: chain C residue 41 LYS 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 705 VAL 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 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 60 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 B 965 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 935 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 = 0.4152 r_free = 0.4152 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120810 restraints weight = 29030.954| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.30 r_work: 0.3365 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 21640 Z= 0.284 Angle : 0.730 12.243 29505 Z= 0.363 Chirality : 0.052 0.526 3514 Planarity : 0.005 0.067 3758 Dihedral : 7.273 82.490 3422 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.71 % Allowed : 19.97 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.15), residues: 2676 helix: 0.38 (0.22), residues: 564 sheet: -0.56 (0.23), residues: 514 loop : -1.94 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.023 0.002 TYR B1067 PHE 0.027 0.002 PHE B1089 TRP 0.024 0.002 TRP B 886 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00699 (21601) covalent geometry : angle 0.71731 (29415) SS BOND : bond 0.00488 ( 27) SS BOND : angle 1.27058 ( 54) hydrogen bonds : bond 0.05256 ( 686) hydrogen bonds : angle 5.62055 ( 1902) link_BETA1-4 : bond 0.01292 ( 3) link_BETA1-4 : angle 4.57786 ( 9) link_NAG-ASN : bond 0.00977 ( 9) link_NAG-ASN : angle 3.32325 ( 27) *********************** 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 222 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 140 time to evaluate : 0.826 Fit side-chains REVERT: A 1123 SER cc_start: 0.8477 (t) cc_final: 0.8275 (p) REVERT: B 203 ILE cc_start: 0.7573 (mt) cc_final: 0.7214 (mp) REVERT: B 314 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8220 (tp-100) REVERT: B 765 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8023 (ttt90) REVERT: B 1111 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: C 265 TYR cc_start: 0.7538 (p90) cc_final: 0.7298 (p90) REVERT: C 787 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7924 (mm-40) outliers start: 82 outliers final: 46 residues processed: 208 average time/residue: 0.4194 time to fit residues: 104.0439 Evaluate side-chains 182 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE 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 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 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 GLN 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 602 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU 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 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 323 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 967 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 221 optimal weight: 0.0370 chunk 268 optimal weight: 0.5980 chunk 233 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 66 HIS B 710 ASN B 965 GLN C 52 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.173573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135779 restraints weight = 28963.695| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.93 r_work: 0.3392 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21640 Z= 0.109 Angle : 0.574 10.969 29505 Z= 0.281 Chirality : 0.045 0.500 3514 Planarity : 0.004 0.066 3758 Dihedral : 6.587 81.774 3422 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.12 % Allowed : 21.83 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2676 helix: 0.85 (0.22), residues: 565 sheet: -0.52 (0.23), residues: 512 loop : -1.81 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.021 0.001 TYR C1138 PHE 0.015 0.001 PHE A1121 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (21601) covalent geometry : angle 0.56148 (29415) SS BOND : bond 0.00200 ( 27) SS BOND : angle 0.80461 ( 54) hydrogen bonds : bond 0.03490 ( 686) hydrogen bonds : angle 5.13240 ( 1902) link_BETA1-4 : bond 0.01054 ( 3) link_BETA1-4 : angle 4.40820 ( 9) link_NAG-ASN : bond 0.00704 ( 9) link_NAG-ASN : angle 2.94551 ( 27) *********************** 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 187 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.6075 (m) cc_final: 0.5767 (p) REVERT: B 177 MET cc_start: 0.6691 (mmp) cc_final: 0.6055 (pp-130) REVERT: B 203 ILE cc_start: 0.7351 (mt) cc_final: 0.6980 (mp) REVERT: B 1111 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: C 265 TYR cc_start: 0.7353 (p90) cc_final: 0.7058 (p90) REVERT: C 323 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8247 (t) REVERT: C 787 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7778 (mm-40) outliers start: 47 outliers final: 25 residues processed: 179 average time/residue: 0.4048 time to fit residues: 87.3118 Evaluate side-chains 163 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 704 SER 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 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 606 ASN 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 1111 GLU 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 429 PHE Chi-restraints excluded: chain C residue 787 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 155 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 268 optimal weight: 0.0070 chunk 82 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137283 restraints weight = 28755.880| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 4.11 r_work: 0.3406 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 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 = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21640 Z= 0.120 Angle : 0.569 10.970 29505 Z= 0.278 Chirality : 0.046 0.536 3514 Planarity : 0.004 0.065 3758 Dihedral : 6.385 79.403 3422 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.03 % Allowed : 21.87 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.16), residues: 2676 helix: 1.06 (0.22), residues: 564 sheet: -0.45 (0.23), residues: 517 loop : -1.71 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE C 817 TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00286 (21601) covalent geometry : angle 0.55591 (29415) SS BOND : bond 0.00214 ( 27) SS BOND : angle 0.86086 ( 54) hydrogen bonds : bond 0.03512 ( 686) hydrogen bonds : angle 4.95961 ( 1902) link_BETA1-4 : bond 0.01166 ( 3) link_BETA1-4 : angle 4.35243 ( 9) link_NAG-ASN : bond 0.00789 ( 9) link_NAG-ASN : angle 2.98561 ( 27) *********************** 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 184 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.6138 (m) cc_final: 0.5832 (p) REVERT: A 935 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: B 177 MET cc_start: 0.6555 (mmp) cc_final: 0.5980 (pp-130) REVERT: B 203 ILE cc_start: 0.7364 (mt) cc_final: 0.6995 (mp) REVERT: B 1111 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: C 265 TYR cc_start: 0.7370 (p90) cc_final: 0.7093 (p90) REVERT: C 323 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8264 (t) REVERT: C 554 GLU cc_start: 0.7626 (pt0) cc_final: 0.6754 (pp20) REVERT: C 787 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7752 (mm-40) outliers start: 45 outliers final: 33 residues processed: 175 average time/residue: 0.4318 time to fit residues: 91.1317 Evaluate side-chains 174 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 994 ASP Chi-restraints excluded: chain A residue 1002 GLN 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 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 606 ASN 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 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 967 SER 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 111 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 270 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 chunk 2 optimal weight: 6.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 710 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137651 restraints weight = 29074.186| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 4.10 r_work: 0.3398 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21640 Z= 0.111 Angle : 0.563 10.987 29505 Z= 0.276 Chirality : 0.045 0.548 3514 Planarity : 0.004 0.065 3758 Dihedral : 6.274 78.349 3422 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.67 % Allowed : 22.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.16), residues: 2676 helix: 1.14 (0.23), residues: 564 sheet: -0.34 (0.23), residues: 511 loop : -1.69 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.015 0.001 PHE A1121 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00262 (21601) covalent geometry : angle 0.54841 (29415) SS BOND : bond 0.00352 ( 27) SS BOND : angle 1.29834 ( 54) hydrogen bonds : bond 0.03353 ( 686) hydrogen bonds : angle 4.89561 ( 1902) link_BETA1-4 : bond 0.01222 ( 3) link_BETA1-4 : angle 4.26627 ( 9) link_NAG-ASN : bond 0.00743 ( 9) link_NAG-ASN : angle 3.08935 ( 27) ********************** 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 177 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.6176 (m) cc_final: 0.5814 (p) REVERT: B 177 MET cc_start: 0.6536 (mmp) cc_final: 0.5972 (pp-130) REVERT: B 203 ILE cc_start: 0.7358 (mt) cc_final: 0.6986 (mp) REVERT: B 1111 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: C 265 TYR cc_start: 0.7345 (p90) cc_final: 0.7068 (p90) REVERT: C 323 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8267 (t) REVERT: C 554 GLU cc_start: 0.7648 (pt0) cc_final: 0.6768 (pp20) REVERT: C 787 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7752 (mm-40) outliers start: 37 outliers final: 30 residues processed: 170 average time/residue: 0.4307 time to fit residues: 87.7512 Evaluate side-chains 166 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 704 SER 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 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 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 606 ASN 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 1106 GLN Chi-restraints excluded: chain B residue 1111 GLU 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 429 PHE Chi-restraints excluded: chain C residue 787 GLN 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 244 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 603 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 = 0.4177 r_free = 0.4177 target = 0.172496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122444 restraints weight = 29220.364| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.33 r_work: 0.3433 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21640 Z= 0.133 Angle : 0.579 10.948 29505 Z= 0.284 Chirality : 0.046 0.538 3514 Planarity : 0.004 0.065 3758 Dihedral : 6.291 76.491 3421 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.94 % Allowed : 22.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.16), residues: 2676 helix: 1.04 (0.22), residues: 565 sheet: -0.45 (0.22), residues: 536 loop : -1.65 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.024 0.001 PHE C 392 TRP 0.016 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (21601) covalent geometry : angle 0.56442 (29415) SS BOND : bond 0.00351 ( 27) SS BOND : angle 1.33433 ( 54) hydrogen bonds : bond 0.03606 ( 686) hydrogen bonds : angle 4.94840 ( 1902) link_BETA1-4 : bond 0.01111 ( 3) link_BETA1-4 : angle 4.26076 ( 9) link_NAG-ASN : bond 0.00789 ( 9) link_NAG-ASN : angle 3.14703 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7093.39 seconds wall clock time: 121 minutes 32.70 seconds (7292.70 seconds total)