Starting phenix.real_space_refine on Sun Sep 13 05:56:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.cif" model { file = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crv_7573/09_2026/6crv_7573.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 111 5.16 5 C 13362 2.51 5 N 3438 2.21 5 O 4125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21036 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "B" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "C" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 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 chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 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 chiralities: 6 Time building chain proxies: 5.45, per 1000 atoms: 0.26 Number of scatterers: 21036 At special positions: 0 Unit cell: (146.26, 149.35, 144.2, 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 111 16.00 O 4125 8.00 N 3438 7.00 C 13362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.00 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.00 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.00 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1304 " - " ASN A 691 " " NAG A1308 " - " ASN A1080 " " NAG A1309 " - " ASN A1116 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A 602 " " NAG B1301 " - " ASN B 65 " " NAG B1304 " - " ASN B 691 " " NAG B1308 " - " ASN B1080 " " NAG B1309 " - " ASN B1116 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B 602 " " NAG C1301 " - " ASN C 65 " " NAG C1304 " - " ASN C 691 " " NAG C1308 " - " ASN C1080 " " NAG C1309 " - " ASN C1116 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C 602 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 783 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN B 269 " " NAG H 1 " - " ASN B 783 " " NAG I 1 " - " ASN B 699 " " NAG J 1 " - " ASN C 269 " " NAG K 1 " - " ASN C 783 " " NAG L 1 " - " ASN C 699 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 24.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE A 870 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.588A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE C 870 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.575A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1013 removed outlier: 3.568A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.800A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.490A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 13.118A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.225A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS B 181 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 203 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG B 183 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 201 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 185 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY B 199 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 187 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 197 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASN B 189 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 195 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.515A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.196A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 823 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.935A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.953A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE C 782 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.367A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2604 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: 4.95 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6362 1.33 - 1.46: 5223 1.46 - 1.58: 9742 1.58 - 1.71: 3 1.71 - 1.83: 153 Bond restraints: 21483 Sorted by residual: bond pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.58e-02 4.01e+03 9.42e+00 bond pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.58e-02 4.01e+03 9.38e+00 ... (remaining 21478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 27652 2.20 - 4.41: 1340 4.41 - 6.61: 180 6.61 - 8.82: 24 8.82 - 11.02: 15 Bond angle restraints: 29211 Sorted by residual: angle pdb=" N GLY C 867 " pdb=" CA GLY C 867 " pdb=" C GLY C 867 " ideal model delta sigma weight residual 110.95 119.29 -8.34 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY B 867 " pdb=" CA GLY B 867 " pdb=" C GLY B 867 " ideal model delta sigma weight residual 110.95 119.27 -8.32 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY A 867 " pdb=" CA GLY A 867 " pdb=" C GLY A 867 " ideal model delta sigma weight residual 110.95 119.26 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 29206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 12012 16.66 - 33.31: 384 33.31 - 49.96: 78 49.96 - 66.62: 9 66.62 - 83.27: 9 Dihedral angle restraints: 12492 sinusoidal: 4818 harmonic: 7674 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.26 83.26 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.25 83.25 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2221 0.057 - 0.115: 1021 0.115 - 0.172: 180 0.172 - 0.230: 31 0.230 - 0.287: 12 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CB VAL A 711 " pdb=" CA VAL A 711 " pdb=" CG1 VAL A 711 " pdb=" CG2 VAL A 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 711 " pdb=" CA VAL C 711 " pdb=" CG1 VAL C 711 " pdb=" CG2 VAL C 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL B 711 " pdb=" CA VAL B 711 " pdb=" CG1 VAL B 711 " pdb=" CG2 VAL B 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3462 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 868 " 0.017 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" CG TRP B 868 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 868 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.017 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 868 " 0.017 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP C 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP C 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 868 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 868 " 0.005 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1339 2.72 - 3.26: 18996 3.26 - 3.81: 32848 3.81 - 4.35: 40034 4.35 - 4.90: 71121 Nonbonded interactions: 164338 Sorted by model distance: nonbonded pdb=" NH2 ARG A 306 " pdb=" OD1 ASP B 727 " model vdw 2.170 3.120 nonbonded pdb=" NH2 ARG B 306 " pdb=" OD1 ASP C 727 " model vdw 2.183 3.120 nonbonded pdb=" OE1 GLU B 999 " pdb=" NH2 ARG C1001 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLU A 999 " pdb=" NH2 ARG B1001 " model vdw 2.278 3.120 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.302 3.040 ... (remaining 164333 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.600 Find NCS groups from input model: 0.650 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.013 0.150 21555 Z= 0.536 Angle : 1.120 11.019 29394 Z= 0.603 Chirality : 0.064 0.287 3465 Planarity : 0.007 0.073 3726 Dihedral : 8.903 70.869 7443 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.26 % Allowed : 0.66 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.13), residues: 2607 helix: -3.57 (0.10), residues: 600 sheet: -0.70 (0.19), residues: 642 loop : -1.98 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B1089 TYR 0.051 0.006 TYR C 197 PHE 0.051 0.005 PHE C 870 TRP 0.047 0.008 TRP B 868 HIS 0.017 0.004 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01282 / 0.54 (21483) covalent geometry : angle 1.09104 / 0.60 (29211) SS BOND : bond 0.00976 / 0.75 ( 33) SS BOND : angle 2.59868 / 1.64 ( 66) hydrogen bonds : bond 0.26465 / 17.32 ( 889) hydrogen bonds : angle 8.47344 / 5.86 ( 2604) link_BETA1-4 : bond 0.01156 / 0.65 ( 12) link_BETA1-4 : angle 4.15933 / 2.83 ( 36) link_NAG-ASN : bond 0.00550 / 0.35 ( 27) link_NAG-ASN : angle 3.51141 / 2.28 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 339 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.7688 (m) cc_final: 0.7314 (p) REVERT: A 89 PHE cc_start: 0.6290 (t80) cc_final: 0.5806 (t80) REVERT: A 868 TRP cc_start: 0.5200 (t-100) cc_final: 0.4887 (t-100) REVERT: A 932 ASP cc_start: 0.7695 (t70) cc_final: 0.7483 (t0) REVERT: B 78 ASN cc_start: 0.6603 (p0) cc_final: 0.6034 (m110) REVERT: B 89 PHE cc_start: 0.6198 (t80) cc_final: 0.5882 (t80) REVERT: B 932 ASP cc_start: 0.7793 (t70) cc_final: 0.7519 (t0) REVERT: C 87 ILE cc_start: 0.8520 (pt) cc_final: 0.8314 (mm) REVERT: C 932 ASP cc_start: 0.7957 (t70) cc_final: 0.7666 (t0) outliers start: 6 outliers final: 2 residues processed: 345 average time/residue: 0.1729 time to fit residues: 89.1725 Evaluate side-chains 181 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 1022 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 883 GLN A1030 HIS A1046 HIS A1095 GLN B 721 ASN B 756 GLN B 786 GLN B 818 GLN B1030 HIS B1046 HIS C 721 ASN C 818 GLN C1030 HIS C1046 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118798 restraints weight = 31180.238| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.19 r_work: 0.3168 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21555 Z= 0.226 Angle : 0.714 9.410 29394 Z= 0.374 Chirality : 0.048 0.252 3465 Planarity : 0.005 0.052 3726 Dihedral : 5.551 38.942 2810 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.23 % Allowed : 4.91 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 2607 helix: -0.41 (0.19), residues: 615 sheet: -0.31 (0.20), residues: 612 loop : -1.81 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 183 TYR 0.018 0.003 TYR C 300 PHE 0.027 0.002 PHE C 83 TRP 0.021 0.002 TRP A 868 HIS 0.006 0.002 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (21483) covalent geometry : angle 0.69676 / 0.37 (29211) SS BOND : bond 0.00529 / 0.38 ( 33) SS BOND : angle 1.98479 / 1.50 ( 66) hydrogen bonds : bond 0.06341 / 4.19 ( 889) hydrogen bonds : angle 5.37659 / 3.74 ( 2604) link_BETA1-4 : bond 0.00348 / 0.19 ( 12) link_BETA1-4 : angle 1.97790 / 1.35 ( 36) link_NAG-ASN : bond 0.00351 / 0.23 ( 27) link_NAG-ASN : angle 2.21354 / 1.44 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.781 Fit side-chains REVERT: A 67 THR cc_start: 0.7064 (m) cc_final: 0.6433 (p) REVERT: A 99 ARG cc_start: 0.6140 (mmt90) cc_final: 0.5842 (mmt90) REVERT: A 721 ASN cc_start: 0.7800 (m-40) cc_final: 0.7429 (m-40) REVERT: A 868 TRP cc_start: 0.5299 (t-100) cc_final: 0.4778 (t-100) REVERT: A 932 ASP cc_start: 0.8439 (t70) cc_final: 0.8146 (t0) REVERT: B 78 ASN cc_start: 0.7262 (p0) cc_final: 0.6224 (m110) REVERT: B 89 PHE cc_start: 0.6889 (t80) cc_final: 0.6369 (t80) REVERT: B 99 ARG cc_start: 0.6081 (mmt90) cc_final: 0.5727 (mtt90) REVERT: B 758 ARG cc_start: 0.7874 (tmm160) cc_final: 0.7507 (ttp80) REVERT: B 932 ASP cc_start: 0.8393 (t70) cc_final: 0.8092 (t0) REVERT: C 89 PHE cc_start: 0.6911 (t80) cc_final: 0.6516 (t80) REVERT: C 99 ARG cc_start: 0.6225 (mmt90) cc_final: 0.5808 (mtt90) REVERT: C 306 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7521 (mpt-90) REVERT: C 758 ARG cc_start: 0.7802 (tmm160) cc_final: 0.7535 (ttp80) REVERT: C 932 ASP cc_start: 0.8501 (t70) cc_final: 0.8220 (t0) outliers start: 28 outliers final: 19 residues processed: 228 average time/residue: 0.1552 time to fit residues: 54.2980 Evaluate side-chains 183 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 212 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.5566 > 50:) chunk 149 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 263 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 GLN A 947 GLN B 947 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120296 restraints weight = 31097.776| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.22 r_work: 0.3187 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21555 Z= 0.138 Angle : 0.600 7.962 29394 Z= 0.314 Chirality : 0.045 0.273 3465 Planarity : 0.004 0.041 3726 Dihedral : 5.094 35.628 2810 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.58 % Allowed : 6.18 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2607 helix: 1.04 (0.21), residues: 615 sheet: -0.36 (0.20), residues: 648 loop : -1.49 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.015 0.002 TYR C 886 PHE 0.023 0.001 PHE A 83 TRP 0.017 0.001 TRP A 868 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21483) covalent geometry : angle 0.58282 / 0.31 (29211) SS BOND : bond 0.00371 / 0.27 ( 33) SS BOND : angle 1.87672 / 1.32 ( 66) hydrogen bonds : bond 0.05273 / 3.51 ( 889) hydrogen bonds : angle 5.11224 / 3.57 ( 2604) link_BETA1-4 : bond 0.00473 / 0.27 ( 12) link_BETA1-4 : angle 1.72549 / 1.19 ( 36) link_NAG-ASN : bond 0.00190 / 0.14 ( 27) link_NAG-ASN : angle 1.94381 / 1.28 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.790 Fit side-chains REVERT: A 67 THR cc_start: 0.7001 (m) cc_final: 0.6419 (p) REVERT: A 89 PHE cc_start: 0.6891 (t80) cc_final: 0.6318 (t80) REVERT: A 99 ARG cc_start: 0.6127 (mmt90) cc_final: 0.5817 (mmt90) REVERT: A 296 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: A 819 TYR cc_start: 0.8001 (p90) cc_final: 0.7439 (p90) REVERT: A 868 TRP cc_start: 0.5098 (t-100) cc_final: 0.4684 (t-100) REVERT: A 932 ASP cc_start: 0.8304 (t70) cc_final: 0.7984 (t0) REVERT: B 67 THR cc_start: 0.6836 (m) cc_final: 0.6131 (p) REVERT: B 78 ASN cc_start: 0.7358 (p0) cc_final: 0.6463 (m110) REVERT: B 87 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 89 PHE cc_start: 0.6857 (t80) cc_final: 0.6324 (t80) REVERT: B 99 ARG cc_start: 0.5945 (mmt90) cc_final: 0.5591 (mtt90) REVERT: B 109 ASN cc_start: 0.6587 (p0) cc_final: 0.6386 (p0) REVERT: B 758 ARG cc_start: 0.7722 (tmm160) cc_final: 0.7366 (ttp80) REVERT: B 932 ASP cc_start: 0.8260 (t70) cc_final: 0.7998 (t0) REVERT: C 89 PHE cc_start: 0.6856 (t80) cc_final: 0.6410 (t80) REVERT: C 99 ARG cc_start: 0.6253 (mmt90) cc_final: 0.5852 (mtt90) REVERT: C 750 SER cc_start: 0.9004 (t) cc_final: 0.8759 (m) REVERT: C 758 ARG cc_start: 0.7634 (tmm160) cc_final: 0.7288 (ttp80) REVERT: C 932 ASP cc_start: 0.8309 (t70) cc_final: 0.7976 (t0) outliers start: 36 outliers final: 22 residues processed: 224 average time/residue: 0.1388 time to fit residues: 48.6233 Evaluate side-chains 191 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 120 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 756 GLN C 947 GLN C1053 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118934 restraints weight = 31158.094| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.23 r_work: 0.3160 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21555 Z= 0.160 Angle : 0.602 7.443 29394 Z= 0.315 Chirality : 0.046 0.249 3465 Planarity : 0.004 0.038 3726 Dihedral : 4.995 36.591 2810 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.84 % Allowed : 6.75 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2607 helix: 1.71 (0.21), residues: 609 sheet: -0.29 (0.20), residues: 663 loop : -1.34 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1073 TYR 0.015 0.002 TYR A 886 PHE 0.028 0.002 PHE B 83 TRP 0.015 0.001 TRP A 868 HIS 0.003 0.001 HIS B1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (21483) covalent geometry : angle 0.58364 / 0.31 (29211) SS BOND : bond 0.00414 / 0.31 ( 33) SS BOND : angle 2.13421 / 1.57 ( 66) hydrogen bonds : bond 0.05192 / 3.45 ( 889) hydrogen bonds : angle 5.03218 / 3.53 ( 2604) link_BETA1-4 : bond 0.00447 / 0.24 ( 12) link_BETA1-4 : angle 1.71004 / 1.18 ( 36) link_NAG-ASN : bond 0.00168 / 0.11 ( 27) link_NAG-ASN : angle 1.89528 / 1.26 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.792 Fit side-chains REVERT: A 67 THR cc_start: 0.7135 (m) cc_final: 0.6506 (p) REVERT: A 89 PHE cc_start: 0.6947 (t80) cc_final: 0.6374 (t80) REVERT: A 99 ARG cc_start: 0.6233 (mmt90) cc_final: 0.5930 (mmt90) REVERT: A 296 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: A 819 TYR cc_start: 0.8048 (p90) cc_final: 0.7461 (p90) REVERT: A 868 TRP cc_start: 0.5158 (t-100) cc_final: 0.4674 (t-100) REVERT: A 932 ASP cc_start: 0.8306 (t70) cc_final: 0.7998 (t0) REVERT: B 67 THR cc_start: 0.6902 (m) cc_final: 0.6253 (p) REVERT: B 78 ASN cc_start: 0.7483 (p0) cc_final: 0.6748 (m-40) REVERT: B 87 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8216 (mp) REVERT: B 89 PHE cc_start: 0.6965 (t80) cc_final: 0.6399 (t80) REVERT: B 99 ARG cc_start: 0.6032 (mmt90) cc_final: 0.5653 (mtt90) REVERT: B 107 MET cc_start: 0.4244 (mpp) cc_final: 0.3746 (mtp) REVERT: B 109 ASN cc_start: 0.7016 (p0) cc_final: 0.6722 (p0) REVERT: B 758 ARG cc_start: 0.7832 (tmm160) cc_final: 0.7560 (ttp80) REVERT: B 932 ASP cc_start: 0.8200 (t70) cc_final: 0.7965 (t0) REVERT: C 89 PHE cc_start: 0.7001 (t80) cc_final: 0.6478 (t80) REVERT: C 99 ARG cc_start: 0.6503 (mmt90) cc_final: 0.6114 (mtt90) REVERT: C 750 SER cc_start: 0.9016 (t) cc_final: 0.8786 (m) REVERT: C 758 ARG cc_start: 0.7687 (tmm160) cc_final: 0.7362 (ttp80) REVERT: C 932 ASP cc_start: 0.8291 (t70) cc_final: 0.7968 (t0) outliers start: 42 outliers final: 31 residues processed: 216 average time/residue: 0.1394 time to fit residues: 48.0567 Evaluate side-chains 198 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 259 optimal weight: 0.5980 chunk 85 optimal weight: 0.0060 chunk 95 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 226 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN C1053 GLN C1088 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121644 restraints weight = 31074.171| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.16 r_work: 0.3202 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 21555 Z= 0.104 Angle : 0.544 7.338 29394 Z= 0.286 Chirality : 0.044 0.264 3465 Planarity : 0.003 0.034 3726 Dihedral : 4.718 32.906 2810 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.71 % Allowed : 7.84 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2607 helix: 2.15 (0.21), residues: 609 sheet: -0.12 (0.20), residues: 630 loop : -1.15 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 965 TYR 0.016 0.001 TYR A 886 PHE 0.027 0.001 PHE B 83 TRP 0.014 0.001 TRP A 868 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21483) covalent geometry : angle 0.52807 / 0.28 (29211) SS BOND : bond 0.00434 / 0.27 ( 33) SS BOND : angle 1.92187 / 1.46 ( 66) hydrogen bonds : bond 0.04232 / 2.82 ( 889) hydrogen bonds : angle 4.81171 / 3.38 ( 2604) link_BETA1-4 : bond 0.00420 / 0.25 ( 12) link_BETA1-4 : angle 1.55167 / 1.07 ( 36) link_NAG-ASN : bond 0.00147 / 0.11 ( 27) link_NAG-ASN : angle 1.69257 / 1.13 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.752 Fit side-chains REVERT: A 67 THR cc_start: 0.7080 (m) cc_final: 0.6444 (p) REVERT: A 89 PHE cc_start: 0.6887 (t80) cc_final: 0.6313 (t80) REVERT: A 99 ARG cc_start: 0.6086 (mmt90) cc_final: 0.5844 (mmt90) REVERT: A 296 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: A 819 TYR cc_start: 0.8012 (p90) cc_final: 0.7489 (p90) REVERT: A 868 TRP cc_start: 0.5049 (t-100) cc_final: 0.4690 (t-100) REVERT: A 932 ASP cc_start: 0.8213 (t70) cc_final: 0.7968 (t0) REVERT: B 67 THR cc_start: 0.6821 (m) cc_final: 0.6186 (p) REVERT: B 78 ASN cc_start: 0.7471 (p0) cc_final: 0.6774 (m-40) REVERT: B 87 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 89 PHE cc_start: 0.6913 (t80) cc_final: 0.6359 (t80) REVERT: B 99 ARG cc_start: 0.6125 (mmt90) cc_final: 0.5722 (mtt90) REVERT: B 109 ASN cc_start: 0.7089 (p0) cc_final: 0.6749 (p0) REVERT: B 758 ARG cc_start: 0.7759 (tmm160) cc_final: 0.7466 (ttp80) REVERT: B 932 ASP cc_start: 0.8076 (t70) cc_final: 0.7828 (t0) REVERT: C 89 PHE cc_start: 0.6907 (t80) cc_final: 0.6435 (t80) REVERT: C 99 ARG cc_start: 0.6564 (mmt90) cc_final: 0.6143 (mtt90) REVERT: C 109 ASN cc_start: 0.6729 (p0) cc_final: 0.6518 (p0) REVERT: C 758 ARG cc_start: 0.7684 (tmm160) cc_final: 0.7365 (ttp80) REVERT: C 932 ASP cc_start: 0.8124 (t70) cc_final: 0.7807 (t0) outliers start: 39 outliers final: 21 residues processed: 228 average time/residue: 0.1366 time to fit residues: 49.5308 Evaluate side-chains 189 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 141 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN C1053 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118884 restraints weight = 31064.996| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.22 r_work: 0.3158 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21555 Z= 0.150 Angle : 0.572 7.394 29394 Z= 0.299 Chirality : 0.045 0.243 3465 Planarity : 0.004 0.034 3726 Dihedral : 4.679 35.907 2809 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.01 % Allowed : 8.45 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2607 helix: 2.27 (0.21), residues: 606 sheet: -0.12 (0.20), residues: 645 loop : -1.10 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1021 TYR 0.015 0.002 TYR A 886 PHE 0.027 0.001 PHE C 83 TRP 0.016 0.001 TRP A 868 HIS 0.003 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (21483) covalent geometry : angle 0.55551 / 0.29 (29211) SS BOND : bond 0.00656 / 0.44 ( 33) SS BOND : angle 2.08941 / 1.50 ( 66) hydrogen bonds : bond 0.04740 / 3.14 ( 889) hydrogen bonds : angle 4.80385 / 3.37 ( 2604) link_BETA1-4 : bond 0.00433 / 0.25 ( 12) link_BETA1-4 : angle 1.66512 / 1.16 ( 36) link_NAG-ASN : bond 0.00131 / 0.09 ( 27) link_NAG-ASN : angle 1.68406 / 1.12 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.708 Fit side-chains REVERT: A 67 THR cc_start: 0.7120 (m) cc_final: 0.6482 (p) REVERT: A 89 PHE cc_start: 0.7018 (t80) cc_final: 0.6475 (t80) REVERT: A 99 ARG cc_start: 0.6132 (mmt90) cc_final: 0.5882 (mmt90) REVERT: A 727 ASP cc_start: 0.6033 (t0) cc_final: 0.5784 (t0) REVERT: A 932 ASP cc_start: 0.8341 (t70) cc_final: 0.8055 (t0) REVERT: B 78 ASN cc_start: 0.7599 (p0) cc_final: 0.6877 (m-40) REVERT: B 87 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (mp) REVERT: B 89 PHE cc_start: 0.7064 (t80) cc_final: 0.6444 (t80) REVERT: B 99 ARG cc_start: 0.6187 (mmt90) cc_final: 0.5805 (mtt90) REVERT: B 109 ASN cc_start: 0.7050 (p0) cc_final: 0.6681 (p0) REVERT: B 758 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7603 (ttp80) REVERT: B 766 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 932 ASP cc_start: 0.8161 (t70) cc_final: 0.7921 (t0) REVERT: C 89 PHE cc_start: 0.7014 (t80) cc_final: 0.6478 (t80) REVERT: C 99 ARG cc_start: 0.6613 (mmt90) cc_final: 0.6167 (mtt90) REVERT: C 109 ASN cc_start: 0.7069 (p0) cc_final: 0.6797 (p0) REVERT: C 151 MET cc_start: 0.4001 (mmm) cc_final: 0.2635 (ttm) REVERT: C 758 ARG cc_start: 0.7715 (tmm160) cc_final: 0.7407 (ttp80) REVERT: C 932 ASP cc_start: 0.8214 (t70) cc_final: 0.7871 (t0) outliers start: 46 outliers final: 34 residues processed: 217 average time/residue: 0.1444 time to fit residues: 49.5168 Evaluate side-chains 205 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 255 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN C1053 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.159722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119579 restraints weight = 31149.555| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.09 r_work: 0.3174 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21555 Z= 0.126 Angle : 0.549 7.339 29394 Z= 0.286 Chirality : 0.044 0.224 3465 Planarity : 0.003 0.034 3726 Dihedral : 4.586 35.481 2809 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.88 % Allowed : 9.15 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2607 helix: 2.41 (0.21), residues: 606 sheet: -0.08 (0.20), residues: 633 loop : -1.01 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 965 TYR 0.013 0.001 TYR A1049 PHE 0.027 0.001 PHE B 83 TRP 0.015 0.001 TRP A 868 HIS 0.002 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21483) covalent geometry : angle 0.53245 / 0.28 (29211) SS BOND : bond 0.00369 / 0.27 ( 33) SS BOND : angle 1.99013 / 1.40 ( 66) hydrogen bonds : bond 0.04363 / 2.90 ( 889) hydrogen bonds : angle 4.72646 / 3.32 ( 2604) link_BETA1-4 : bond 0.00441 / 0.25 ( 12) link_BETA1-4 : angle 1.58488 / 1.10 ( 36) link_NAG-ASN : bond 0.00109 / 0.08 ( 27) link_NAG-ASN : angle 1.63343 / 1.08 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.726 Fit side-chains REVERT: A 53 TYR cc_start: 0.8604 (t80) cc_final: 0.8268 (t80) REVERT: A 67 THR cc_start: 0.7128 (m) cc_final: 0.6507 (p) REVERT: A 89 PHE cc_start: 0.7075 (t80) cc_final: 0.6531 (t80) REVERT: A 99 ARG cc_start: 0.6100 (mmt90) cc_final: 0.5850 (mmt90) REVERT: A 932 ASP cc_start: 0.8290 (t70) cc_final: 0.8073 (t0) REVERT: A 965 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7301 (tpp-160) REVERT: B 67 THR cc_start: 0.7024 (m) cc_final: 0.6423 (p) REVERT: B 78 ASN cc_start: 0.7481 (p0) cc_final: 0.6820 (m-40) REVERT: B 89 PHE cc_start: 0.7162 (t80) cc_final: 0.6543 (t80) REVERT: B 99 ARG cc_start: 0.6223 (mmt90) cc_final: 0.5790 (mtt90) REVERT: B 109 ASN cc_start: 0.7109 (p0) cc_final: 0.6745 (p0) REVERT: B 758 ARG cc_start: 0.7878 (tmm160) cc_final: 0.7597 (ttp80) REVERT: B 932 ASP cc_start: 0.8120 (t70) cc_final: 0.7876 (t0) REVERT: C 89 PHE cc_start: 0.7013 (t80) cc_final: 0.6482 (t80) REVERT: C 99 ARG cc_start: 0.6631 (mmt90) cc_final: 0.6155 (mtt90) REVERT: C 107 MET cc_start: 0.4841 (mpp) cc_final: 0.4057 (mtt) REVERT: C 109 ASN cc_start: 0.7061 (p0) cc_final: 0.6759 (p0) REVERT: C 151 MET cc_start: 0.4235 (mmm) cc_final: 0.2745 (ttm) REVERT: C 758 ARG cc_start: 0.7715 (tmm160) cc_final: 0.7415 (ttp80) REVERT: C 932 ASP cc_start: 0.8195 (t70) cc_final: 0.7857 (t0) outliers start: 43 outliers final: 30 residues processed: 211 average time/residue: 0.1450 time to fit residues: 48.1672 Evaluate side-chains 196 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 160 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 247 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN B 189 ASN C1053 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120289 restraints weight = 31263.435| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.22 r_work: 0.3183 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21555 Z= 0.110 Angle : 0.532 7.456 29394 Z= 0.278 Chirality : 0.044 0.213 3465 Planarity : 0.003 0.034 3726 Dihedral : 4.471 33.116 2809 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.53 % Allowed : 10.16 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2607 helix: 2.56 (0.21), residues: 606 sheet: -0.02 (0.20), residues: 633 loop : -0.95 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 306 TYR 0.018 0.001 TYR A 886 PHE 0.025 0.001 PHE C 83 TRP 0.014 0.001 TRP A 868 HIS 0.002 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21483) covalent geometry : angle 0.51711 / 0.27 (29211) SS BOND : bond 0.00319 / 0.23 ( 33) SS BOND : angle 1.80322 / 1.27 ( 66) hydrogen bonds : bond 0.04120 / 2.73 ( 889) hydrogen bonds : angle 4.65302 / 3.26 ( 2604) link_BETA1-4 : bond 0.00445 / 0.25 ( 12) link_BETA1-4 : angle 1.55316 / 1.08 ( 36) link_NAG-ASN : bond 0.00098 / 0.07 ( 27) link_NAG-ASN : angle 1.55627 / 1.04 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.717 Fit side-chains REVERT: A 53 TYR cc_start: 0.8577 (t80) cc_final: 0.8245 (t80) REVERT: A 67 THR cc_start: 0.7091 (m) cc_final: 0.6446 (p) REVERT: A 89 PHE cc_start: 0.7092 (t80) cc_final: 0.6564 (t80) REVERT: A 99 ARG cc_start: 0.6102 (mmt90) cc_final: 0.5848 (mmt90) REVERT: A 231 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6684 (p90) REVERT: A 560 ASP cc_start: 0.8387 (p0) cc_final: 0.8105 (t0) REVERT: A 868 TRP cc_start: 0.5448 (t-100) cc_final: 0.5129 (t-100) REVERT: A 932 ASP cc_start: 0.8294 (t70) cc_final: 0.8086 (t0) REVERT: A 965 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7239 (tpp-160) REVERT: B 67 THR cc_start: 0.7038 (m) cc_final: 0.6462 (p) REVERT: B 78 ASN cc_start: 0.7581 (p0) cc_final: 0.6975 (m110) REVERT: B 89 PHE cc_start: 0.7141 (t80) cc_final: 0.6498 (t80) REVERT: B 99 ARG cc_start: 0.6236 (mmt90) cc_final: 0.5803 (mtt90) REVERT: B 109 ASN cc_start: 0.7104 (p0) cc_final: 0.6724 (p0) REVERT: B 256 TYR cc_start: 0.7875 (m-80) cc_final: 0.7547 (m-80) REVERT: B 758 ARG cc_start: 0.7856 (tmm160) cc_final: 0.7580 (ttp80) REVERT: B 932 ASP cc_start: 0.8083 (t70) cc_final: 0.7834 (t0) REVERT: B 965 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7531 (tpp-160) REVERT: C 89 PHE cc_start: 0.7017 (t80) cc_final: 0.6485 (t80) REVERT: C 99 ARG cc_start: 0.6595 (mmt90) cc_final: 0.6105 (mtt90) REVERT: C 107 MET cc_start: 0.4883 (mpp) cc_final: 0.4114 (mtt) REVERT: C 109 ASN cc_start: 0.7055 (p0) cc_final: 0.6727 (p0) REVERT: C 151 MET cc_start: 0.4285 (mmm) cc_final: 0.2827 (ttm) REVERT: C 643 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7014 (p0) REVERT: C 758 ARG cc_start: 0.7697 (tmm160) cc_final: 0.7423 (ttp80) REVERT: C 932 ASP cc_start: 0.8092 (t70) cc_final: 0.7737 (t0) REVERT: C 965 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7310 (tpp-160) outliers start: 35 outliers final: 28 residues processed: 204 average time/residue: 0.1450 time to fit residues: 46.6622 Evaluate side-chains 193 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118124 restraints weight = 31063.659| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.14 r_work: 0.3160 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21555 Z= 0.142 Angle : 0.561 8.179 29394 Z= 0.292 Chirality : 0.045 0.221 3465 Planarity : 0.003 0.034 3726 Dihedral : 4.547 35.830 2809 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 9.94 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2607 helix: 2.50 (0.21), residues: 606 sheet: -0.05 (0.20), residues: 633 loop : -0.95 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.019 0.001 TYR C 886 PHE 0.027 0.001 PHE B 83 TRP 0.016 0.001 TRP A 868 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (21483) covalent geometry : angle 0.54562 / 0.29 (29211) SS BOND : bond 0.00391 / 0.29 ( 33) SS BOND : angle 1.99769 / 1.40 ( 66) hydrogen bonds : bond 0.04539 / 3.01 ( 889) hydrogen bonds : angle 4.67784 / 3.28 ( 2604) link_BETA1-4 : bond 0.00436 / 0.25 ( 12) link_BETA1-4 : angle 1.61248 / 1.12 ( 36) link_NAG-ASN : bond 0.00105 / 0.07 ( 27) link_NAG-ASN : angle 1.57638 / 1.05 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.840 Fit side-chains REVERT: A 67 THR cc_start: 0.7111 (m) cc_final: 0.6476 (p) REVERT: A 89 PHE cc_start: 0.7011 (t80) cc_final: 0.6528 (t80) REVERT: A 99 ARG cc_start: 0.6166 (mmt90) cc_final: 0.5908 (mmt90) REVERT: A 231 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6770 (p90) REVERT: A 932 ASP cc_start: 0.8325 (t70) cc_final: 0.8113 (t0) REVERT: A 965 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7270 (tpp-160) REVERT: B 67 THR cc_start: 0.7093 (m) cc_final: 0.6530 (p) REVERT: B 78 ASN cc_start: 0.7664 (p0) cc_final: 0.7047 (m-40) REVERT: B 99 ARG cc_start: 0.6331 (mmt90) cc_final: 0.5946 (mtt90) REVERT: B 109 ASN cc_start: 0.7260 (p0) cc_final: 0.6876 (p0) REVERT: B 256 TYR cc_start: 0.7980 (m-80) cc_final: 0.7679 (m-80) REVERT: B 560 ASP cc_start: 0.8426 (p0) cc_final: 0.8129 (t0) REVERT: B 758 ARG cc_start: 0.7884 (tmm160) cc_final: 0.7596 (ttp80) REVERT: B 932 ASP cc_start: 0.8159 (t70) cc_final: 0.7909 (t0) REVERT: B 965 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7525 (tpp-160) REVERT: C 99 ARG cc_start: 0.6683 (mmt90) cc_final: 0.6198 (mtt90) REVERT: C 107 MET cc_start: 0.4937 (mpp) cc_final: 0.4164 (mtt) REVERT: C 109 ASN cc_start: 0.7119 (p0) cc_final: 0.6850 (p0) REVERT: C 151 MET cc_start: 0.4645 (mmm) cc_final: 0.2926 (ttm) REVERT: C 560 ASP cc_start: 0.8410 (p0) cc_final: 0.8091 (t0) REVERT: C 643 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7050 (p0) REVERT: C 758 ARG cc_start: 0.7747 (tmm160) cc_final: 0.7466 (ttp80) REVERT: C 932 ASP cc_start: 0.8144 (t70) cc_final: 0.7787 (t0) REVERT: C 965 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.7299 (tpp-160) outliers start: 37 outliers final: 31 residues processed: 204 average time/residue: 0.1394 time to fit residues: 45.0563 Evaluate side-chains 196 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 206 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 69 optimal weight: 0.0010 chunk 49 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 661 HIS A 818 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 599 GLN B 818 GLN B1088 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 756 GLN C 818 GLN C1053 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116116 restraints weight = 31180.029| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.65 r_work: 0.3089 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 21555 Z= 0.228 Angle : 0.645 8.745 29394 Z= 0.335 Chirality : 0.048 0.240 3465 Planarity : 0.004 0.035 3726 Dihedral : 4.959 46.769 2809 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.66 % Allowed : 10.12 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2607 helix: 2.14 (0.21), residues: 606 sheet: -0.18 (0.21), residues: 627 loop : -1.12 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1089 TYR 0.019 0.002 TYR A 886 PHE 0.028 0.002 PHE B 83 TRP 0.022 0.002 TRP A 868 HIS 0.005 0.001 HIS C1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (21483) covalent geometry : angle 0.62561 / 0.33 (29211) SS BOND : bond 0.00559 / 0.42 ( 33) SS BOND : angle 2.50343 / 1.74 ( 66) hydrogen bonds : bond 0.05653 / 3.75 ( 889) hydrogen bonds : angle 4.91034 / 3.44 ( 2604) link_BETA1-4 : bond 0.00447 / 0.25 ( 12) link_BETA1-4 : angle 1.79212 / 1.25 ( 36) link_NAG-ASN : bond 0.00201 / 0.14 ( 27) link_NAG-ASN : angle 1.81130 / 1.18 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.837 Fit side-chains REVERT: A 67 THR cc_start: 0.7194 (m) cc_final: 0.6562 (p) REVERT: A 99 ARG cc_start: 0.6289 (mmt90) cc_final: 0.6048 (mmt90) REVERT: A 151 MET cc_start: 0.4592 (mmm) cc_final: 0.2708 (ttm) REVERT: A 231 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 560 ASP cc_start: 0.8496 (p0) cc_final: 0.8155 (t0) REVERT: A 932 ASP cc_start: 0.8468 (t70) cc_final: 0.8216 (t0) REVERT: A 965 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7271 (tpp-160) REVERT: B 67 THR cc_start: 0.7229 (m) cc_final: 0.6661 (p) REVERT: B 78 ASN cc_start: 0.7736 (p0) cc_final: 0.7220 (m-40) REVERT: B 99 ARG cc_start: 0.6396 (mmt90) cc_final: 0.5986 (mtt90) REVERT: B 109 ASN cc_start: 0.7029 (p0) cc_final: 0.6705 (p0) REVERT: B 151 MET cc_start: 0.4516 (mmm) cc_final: 0.3695 (tpt) REVERT: B 256 TYR cc_start: 0.7963 (m-80) cc_final: 0.7657 (m-80) REVERT: B 560 ASP cc_start: 0.8501 (p0) cc_final: 0.8160 (t0) REVERT: B 758 ARG cc_start: 0.8001 (tmm160) cc_final: 0.7704 (ttp80) REVERT: B 932 ASP cc_start: 0.8447 (t70) cc_final: 0.8226 (t0) REVERT: C 99 ARG cc_start: 0.6723 (mmt90) cc_final: 0.6249 (mtt90) REVERT: C 107 MET cc_start: 0.4833 (mpp) cc_final: 0.4016 (mtt) REVERT: C 109 ASN cc_start: 0.7129 (p0) cc_final: 0.6863 (p0) REVERT: C 151 MET cc_start: 0.4592 (mmm) cc_final: 0.2815 (ttm) REVERT: C 560 ASP cc_start: 0.8485 (p0) cc_final: 0.8136 (t0) REVERT: C 756 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8197 (mp-120) REVERT: C 758 ARG cc_start: 0.7889 (tmm160) cc_final: 0.7628 (ttp80) REVERT: C 932 ASP cc_start: 0.8501 (t70) cc_final: 0.8174 (t0) REVERT: C 965 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7323 (tpp-160) outliers start: 38 outliers final: 33 residues processed: 203 average time/residue: 0.1444 time to fit residues: 45.6844 Evaluate side-chains 201 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115930 restraints weight = 31073.380| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.24 r_work: 0.3109 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 21555 Z= 0.239 Angle : 0.785 59.076 29394 Z= 0.433 Chirality : 0.047 0.235 3465 Planarity : 0.004 0.035 3726 Dihedral : 4.958 46.757 2809 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.71 % Allowed : 10.47 % Favored : 87.82 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2607 helix: 2.11 (0.21), residues: 606 sheet: -0.19 (0.21), residues: 627 loop : -1.13 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.016 0.002 TYR A 886 PHE 0.027 0.002 PHE B 83 TRP 0.021 0.002 TRP A 868 HIS 0.005 0.001 HIS C1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (21483) covalent geometry : angle 0.77053 / 0.43 (29211) SS BOND : bond 0.00562 / 0.42 ( 33) SS BOND : angle 2.47129 / 1.72 ( 66) hydrogen bonds : bond 0.05690 / 3.75 ( 889) hydrogen bonds : angle 4.91287 / 3.44 ( 2604) link_BETA1-4 : bond 0.00368 / 0.22 ( 12) link_BETA1-4 : angle 1.81164 / 1.26 ( 36) link_NAG-ASN : bond 0.00194 / 0.13 ( 27) link_NAG-ASN : angle 1.81157 / 1.18 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.24 seconds wall clock time: 80 minutes 44.45 seconds (4844.45 seconds total)