Starting phenix.real_space_refine on Mon Mar 18 07:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q72_18201/03_2024/8q72_18201_trim_updated.pdb" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 168 5.49 5 S 86 5.16 5 C 26378 2.51 5 N 7820 2.21 5 O 8538 1.98 5 H 41352 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "F TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 895": "OD1" <-> "OD2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 943": "OE1" <-> "OE2" Residue "G PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J ASP 210": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84342 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 11881 Classifications: {'peptide': 750} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 732} Chain breaks: 1 Chain: "B" Number of atoms: 11880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 11880 Classifications: {'peptide': 750} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 732} Chain breaks: 1 Chain: "C" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3173 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3172 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 7532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7532 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 13, 'TRANS': 452} Chain breaks: 1 Chain: "F" Number of atoms: 11881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 11881 Classifications: {'peptide': 750} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 732} Chain breaks: 1 Chain: "G" Number of atoms: 11880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 11880 Classifications: {'peptide': 750} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 732} Chain breaks: 1 Chain: "H" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3173 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "I" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3172 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "J" Number of atoms: 7532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7532 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 13, 'TRANS': 452} Chain breaks: 1 Chain: "M" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1917 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain: "N" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1917 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain: "P" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 1281 Classifications: {'DNA': 40} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 39} Chain: "Q" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 1281 Classifications: {'DNA': 40} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 39} Chain: "R" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 1281 Classifications: {'DNA': 40} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 39} Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 1281 Classifications: {'DNA': 40} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.97, per 1000 atoms: 0.32 Number of scatterers: 84342 At special positions: 0 Unit cell: (320.38, 250.66, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 168 15.00 O 8538 8.00 N 7820 7.00 C 26378 6.00 H 41352 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 57.76 Conformation dependent library (CDL) restraints added in 5.9 seconds 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 28 sheets defined 58.8% alpha, 8.6% beta 80 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 34.99 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 removed outlier: 3.551A pdb=" N ASP A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.674A pdb=" N ASN A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 232 through 342 removed outlier: 4.077A pdb=" N ALA A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 3.589A pdb=" N GLN A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.525A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 743 removed outlier: 4.379A pdb=" N GLN A 743 " --> pdb=" O GLN A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 765 through 807 removed outlier: 4.678A pdb=" N ARG A 769 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A 787 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 841 through 882 removed outlier: 4.726A pdb=" N ASP A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.877A pdb=" N ARG A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 942 removed outlier: 4.077A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 986 through 1004 removed outlier: 3.635A pdb=" N ILE A 991 " --> pdb=" O GLY A 987 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1041 removed outlier: 3.514A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1037 " --> pdb=" O GLY A1033 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.567A pdb=" N SER B 5 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 6 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 4.235A pdb=" N LEU B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 201 through 210 removed outlier: 4.800A pdb=" N ASN B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 232 through 342 removed outlier: 3.622A pdb=" N GLU B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Proline residue: B 264 - end of helix removed outlier: 3.895A pdb=" N LEU B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.710A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 743 removed outlier: 3.521A pdb=" N ALA B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN B 743 " --> pdb=" O GLN B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 763 through 807 Proline residue: B 766 - end of helix removed outlier: 4.780A pdb=" N ARG B 769 " --> pdb=" O PRO B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 834 Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 836 through 854 removed outlier: 3.504A pdb=" N ASP B 853 " --> pdb=" O ASN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 883 removed outlier: 3.728A pdb=" N ASN B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 882 " --> pdb=" O ASN B 878 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 919 removed outlier: 3.782A pdb=" N ALA B 916 " --> pdb=" O ARG B 912 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 943 removed outlier: 3.827A pdb=" N GLN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 Processing helix chain 'B' and resid 956 through 959 Processing helix chain 'B' and resid 990 through 1004 Processing helix chain 'B' and resid 1029 through 1041 removed outlier: 3.585A pdb=" N GLY B1033 " --> pdb=" O HIS B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1060 removed outlier: 4.842A pdb=" N ASP B1060 " --> pdb=" O ARG B1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 77 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 127 through 147 Processing helix chain 'C' and resid 158 through 169 Proline residue: C 163 - end of helix removed outlier: 4.412A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.699A pdb=" N LEU C 213 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 67 through 74 Processing helix chain 'D' and resid 77 through 87 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 158 through 169 Proline residue: D 163 - end of helix removed outlier: 4.140A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 217 through 232 Processing helix chain 'E' and resid 2 through 15 removed outlier: 4.672A pdb=" N THR E 9 " --> pdb=" O ARG E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 removed outlier: 3.614A pdb=" N ALA E 26 " --> pdb=" O TRP E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 43 Proline residue: E 31 - end of helix removed outlier: 3.713A pdb=" N GLU E 42 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.636A pdb=" N HIS E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 91 Proline residue: E 77 - end of helix Processing helix chain 'E' and resid 105 through 116 removed outlier: 3.651A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 178 through 218 removed outlier: 3.545A pdb=" N VAL E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 183 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 239 removed outlier: 3.552A pdb=" N LEU E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 255 removed outlier: 3.645A pdb=" N GLN E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG E 255 " --> pdb=" O GLN E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 removed outlier: 3.697A pdb=" N LYS E 261 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N MET E 263 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 264 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 271 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 282 through 317 removed outlier: 3.652A pdb=" N TRP E 290 " --> pdb=" O HIS E 286 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 291 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 292 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN E 304 " --> pdb=" O GLN E 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 308 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER E 309 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY E 315 " --> pdb=" O ARG E 311 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 341 removed outlier: 3.744A pdb=" N ARG E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 399 through 406 removed outlier: 4.137A pdb=" N ALA E 404 " --> pdb=" O ASP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 424 removed outlier: 3.582A pdb=" N LEU E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 423 " --> pdb=" O GLN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 436 Processing helix chain 'E' and resid 443 through 456 Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'F' and resid 2 through 5 Processing helix chain 'F' and resid 49 through 59 removed outlier: 3.556A pdb=" N THR F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 153 through 162 removed outlier: 4.534A pdb=" N ASN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.685A pdb=" N PHE F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 207 removed outlier: 4.508A pdb=" N ASN F 206 " --> pdb=" O PHE F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 213 removed outlier: 3.982A pdb=" N LYS F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 220 No H-bonds generated for 'chain 'F' and resid 217 through 220' Processing helix chain 'F' and resid 232 through 342 removed outlier: 4.061A pdb=" N ALA F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) Proline residue: F 264 - end of helix removed outlier: 3.557A pdb=" N LYS F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA F 280 " --> pdb=" O GLU F 276 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP F 281 " --> pdb=" O ARG F 277 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP F 282 " --> pdb=" O GLN F 278 " (cutoff:3.500A) Proline residue: F 290 - end of helix removed outlier: 3.757A pdb=" N HIS F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU F 341 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 743 removed outlier: 3.513A pdb=" N ALA F 715 " --> pdb=" O LYS F 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 736 " --> pdb=" O ALA F 732 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN F 743 " --> pdb=" O GLN F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 756 Processing helix chain 'F' and resid 765 through 807 removed outlier: 4.480A pdb=" N ARG F 769 " --> pdb=" O PRO F 766 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS F 787 " --> pdb=" O GLU F 784 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 834 Processing helix chain 'F' and resid 837 through 839 No H-bonds generated for 'chain 'F' and resid 837 through 839' Processing helix chain 'F' and resid 841 through 882 removed outlier: 4.740A pdb=" N ASP F 846 " --> pdb=" O ASN F 842 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 847 " --> pdb=" O ARG F 843 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN F 849 " --> pdb=" O LEU F 845 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 860 " --> pdb=" O VAL F 856 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS F 862 " --> pdb=" O GLN F 858 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU F 864 " --> pdb=" O LEU F 860 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL F 867 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 868 " --> pdb=" O GLU F 864 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 869 " --> pdb=" O HIS F 865 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU F 872 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN F 875 " --> pdb=" O GLU F 871 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 876 " --> pdb=" O GLU F 872 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 877 " --> pdb=" O ARG F 873 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE F 882 " --> pdb=" O ASN F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 902 through 918 removed outlier: 3.872A pdb=" N ARG F 918 " --> pdb=" O LEU F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 943 removed outlier: 4.126A pdb=" N VAL F 935 " --> pdb=" O LEU F 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F 937 " --> pdb=" O VAL F 933 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 938 " --> pdb=" O LEU F 934 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 952 Processing helix chain 'F' and resid 956 through 958 No H-bonds generated for 'chain 'F' and resid 956 through 958' Processing helix chain 'F' and resid 986 through 1004 removed outlier: 3.555A pdb=" N ILE F 991 " --> pdb=" O GLY F 987 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER F 994 " --> pdb=" O GLU F 990 " (cutoff:3.500A) Processing helix chain 'F' and resid 1029 through 1041 removed outlier: 3.653A pdb=" N GLY F1033 " --> pdb=" O HIS F1029 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG F1034 " --> pdb=" O ALA F1030 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F1035 " --> pdb=" O VAL F1031 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F1037 " --> pdb=" O GLY F1033 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F1040 " --> pdb=" O ILE F1036 " (cutoff:3.500A) Processing helix chain 'F' and resid 1055 through 1060 removed outlier: 3.602A pdb=" N ASP F1060 " --> pdb=" O ARG F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1094 Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.524A pdb=" N GLY G 6 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 removed outlier: 3.826A pdb=" N VAL G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 153 through 162 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 184 through 195 Processing helix chain 'G' and resid 200 through 210 removed outlier: 5.251A pdb=" N LEU G 205 " --> pdb=" O PHE G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 224 Processing helix chain 'G' and resid 232 through 342 removed outlier: 3.773A pdb=" N GLY G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU G 253 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN G 258 " --> pdb=" O THR G 254 " (cutoff:3.500A) Proline residue: G 264 - end of helix removed outlier: 3.931A pdb=" N LEU G 267 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 281 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) Proline residue: G 290 - end of helix removed outlier: 3.758A pdb=" N PHE G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 310 " --> pdb=" O ASN G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 743 removed outlier: 3.908A pdb=" N SER G 707 " --> pdb=" O GLN G 703 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU G 708 " --> pdb=" O THR G 704 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU G 709 " --> pdb=" O ILE G 705 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR G 740 " --> pdb=" O LYS G 736 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN G 743 " --> pdb=" O GLN G 739 " (cutoff:3.500A) Processing helix chain 'G' and resid 747 through 756 Processing helix chain 'G' and resid 763 through 807 Proline residue: G 766 - end of helix removed outlier: 4.823A pdb=" N ARG G 769 " --> pdb=" O PRO G 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 819 through 834 Proline residue: G 823 - end of helix Processing helix chain 'G' and resid 836 through 853 Processing helix chain 'G' and resid 856 through 883 removed outlier: 3.513A pdb=" N ASN G 875 " --> pdb=" O GLU G 871 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 876 " --> pdb=" O GLU G 872 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE G 882 " --> pdb=" O ASN G 878 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG G 883 " --> pdb=" O GLU G 879 " (cutoff:3.500A) Processing helix chain 'G' and resid 903 through 919 removed outlier: 3.793A pdb=" N ALA G 916 " --> pdb=" O ARG G 912 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 918 " --> pdb=" O LEU G 914 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE G 919 " --> pdb=" O ASN G 915 " (cutoff:3.500A) Processing helix chain 'G' and resid 925 through 943 removed outlier: 3.513A pdb=" N GLN G 937 " --> pdb=" O VAL G 933 " (cutoff:3.500A) Processing helix chain 'G' and resid 948 through 954 Processing helix chain 'G' and resid 956 through 959 Processing helix chain 'G' and resid 990 through 1005 Processing helix chain 'G' and resid 1029 through 1042 removed outlier: 3.618A pdb=" N GLY G1033 " --> pdb=" O HIS G1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 1055 through 1060 removed outlier: 4.794A pdb=" N ASP G1060 " --> pdb=" O ARG G1056 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 77 through 87 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 114 through 116 No H-bonds generated for 'chain 'H' and resid 114 through 116' Processing helix chain 'H' and resid 127 through 147 Processing helix chain 'H' and resid 158 through 169 Proline residue: H 163 - end of helix removed outlier: 4.709A pdb=" N TYR H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 191 Processing helix chain 'H' and resid 208 through 213 removed outlier: 3.564A pdb=" N LEU H 213 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 233 Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 63 through 75 Proline residue: I 67 - end of helix Processing helix chain 'I' and resid 77 through 87 Proline residue: I 86 - end of helix Processing helix chain 'I' and resid 127 through 146 Processing helix chain 'I' and resid 158 through 169 Proline residue: I 163 - end of helix removed outlier: 4.064A pdb=" N TYR I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 191 Processing helix chain 'I' and resid 208 through 212 Processing helix chain 'I' and resid 216 through 232 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.951A pdb=" N GLU J 10 " --> pdb=" O ARG J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 24 Processing helix chain 'J' and resid 28 through 43 Proline residue: J 31 - end of helix removed outlier: 3.706A pdb=" N GLU J 42 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.641A pdb=" N HIS J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 91 Proline residue: J 77 - end of helix Processing helix chain 'J' and resid 105 through 116 removed outlier: 3.680A pdb=" N VAL J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER J 116 " --> pdb=" O THR J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 178 through 218 removed outlier: 3.747A pdb=" N VAL J 182 " --> pdb=" O THR J 178 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU J 183 " --> pdb=" O HIS J 179 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG J 196 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA J 197 " --> pdb=" O SER J 193 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE J 199 " --> pdb=" O LEU J 195 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG J 200 " --> pdb=" O ARG J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 237 removed outlier: 3.530A pdb=" N LEU J 231 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU J 232 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 255 removed outlier: 3.569A pdb=" N GLN J 252 " --> pdb=" O ASP J 248 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN J 253 " --> pdb=" O SER J 249 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 254 " --> pdb=" O PHE J 250 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG J 255 " --> pdb=" O GLN J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 272 Processing helix chain 'J' and resid 274 through 279 Processing helix chain 'J' and resid 282 through 317 removed outlier: 3.663A pdb=" N TRP J 290 " --> pdb=" O HIS J 286 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU J 291 " --> pdb=" O ASP J 287 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL J 292 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS J 293 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 300 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR J 301 " --> pdb=" O ASP J 297 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL J 302 " --> pdb=" O GLU J 298 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN J 304 " --> pdb=" O GLN J 300 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER J 309 " --> pdb=" O ALA J 305 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL J 313 " --> pdb=" O SER J 309 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG J 314 " --> pdb=" O GLU J 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 315 " --> pdb=" O ARG J 311 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE J 316 " --> pdb=" O ASP J 312 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 341 removed outlier: 3.623A pdb=" N ARG J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS J 341 " --> pdb=" O ASN J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 350 No H-bonds generated for 'chain 'J' and resid 347 through 350' Processing helix chain 'J' and resid 369 through 371 No H-bonds generated for 'chain 'J' and resid 369 through 371' Processing helix chain 'J' and resid 399 through 405 removed outlier: 4.114A pdb=" N ALA J 404 " --> pdb=" O ASP J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 424 Processing helix chain 'J' and resid 430 through 437 Processing helix chain 'J' and resid 443 through 456 Processing helix chain 'J' and resid 489 through 494 Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 42 through 45 No H-bonds generated for 'chain 'M' and resid 42 through 45' Processing helix chain 'M' and resid 49 through 60 Processing helix chain 'M' and resid 92 through 99 Processing helix chain 'M' and resid 102 through 116 removed outlier: 3.623A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 15 Processing helix chain 'N' and resid 18 through 26 Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 42 through 45 No H-bonds generated for 'chain 'N' and resid 42 through 45' Processing helix chain 'N' and resid 49 through 61 Processing helix chain 'N' and resid 92 through 99 Processing helix chain 'N' and resid 102 through 114 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.972A pdb=" N ARG A 17 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 124 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 181 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1047 through 1049 removed outlier: 6.545A pdb=" N THR A 39 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 40 " --> pdb=" O SER A1064 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 890 through 898 removed outlier: 3.543A pdb=" N ALA A 963 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 976 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 968 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 974 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.758A pdb=" N THR B 113 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE B 18 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA B 111 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 20 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 109 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.749A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B1048 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 890 through 898 Processing sheet with id= G, first strand: chain 'B' and resid 1064 through 1071 removed outlier: 3.642A pdb=" N ALA B1078 " --> pdb=" O VAL B1067 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS B1069 " --> pdb=" O ASN B1076 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 60 through 62 Processing sheet with id= I, first strand: chain 'C' and resid 155 through 157 Processing sheet with id= J, first strand: chain 'D' and resid 60 through 62 Processing sheet with id= K, first strand: chain 'D' and resid 155 through 157 Processing sheet with id= L, first strand: chain 'E' and resid 461 through 471 removed outlier: 7.319A pdb=" N SER E 463 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU E 482 " --> pdb=" O SER E 463 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ARG E 465 " --> pdb=" O PHE E 480 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N PHE E 480 " --> pdb=" O ARG E 465 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N PHE E 467 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N TRP E 478 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 29 through 33 removed outlier: 3.720A pdb=" N ALA F 32 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG F 17 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 124 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR F 181 " --> pdb=" O TRP F 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 40 through 42 Processing sheet with id= O, first strand: chain 'F' and resid 890 through 896 removed outlier: 3.643A pdb=" N GLU F 976 " --> pdb=" O VAL F 966 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP F 968 " --> pdb=" O VAL F 974 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL F 974 " --> pdb=" O ASP F 968 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 29 through 33 removed outlier: 6.768A pdb=" N THR G 113 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE G 18 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA G 111 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU G 20 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY G 109 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 39 through 42 removed outlier: 3.752A pdb=" N THR G 39 " --> pdb=" O ALA G1046 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE G1048 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 890 through 898 Processing sheet with id= S, first strand: chain 'G' and resid 1064 through 1071 removed outlier: 3.568A pdb=" N ALA G1078 " --> pdb=" O VAL G1067 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS G1069 " --> pdb=" O ASN G1076 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G1076 " --> pdb=" O HIS G1069 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 60 through 62 Processing sheet with id= U, first strand: chain 'H' and resid 155 through 157 Processing sheet with id= V, first strand: chain 'I' and resid 60 through 62 Processing sheet with id= W, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= X, first strand: chain 'J' and resid 461 through 471 removed outlier: 7.326A pdb=" N SER J 463 " --> pdb=" O LEU J 482 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N LEU J 482 " --> pdb=" O SER J 463 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N ARG J 465 " --> pdb=" O PHE J 480 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N PHE J 480 " --> pdb=" O ARG J 465 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N PHE J 467 " --> pdb=" O TRP J 478 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N TRP J 478 " --> pdb=" O PHE J 467 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 33 through 36 Processing sheet with id= Z, first strand: chain 'M' and resid 69 through 72 Processing sheet with id= AA, first strand: chain 'N' and resid 33 through 36 Processing sheet with id= AB, first strand: chain 'N' and resid 69 through 72 2156 hydrogen bonds defined for protein. 5508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 160 hydrogen bonds 320 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 32.26 Time building geometry restraints manager: 60.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 41328 1.03 - 1.23: 822 1.23 - 1.43: 17907 1.43 - 1.63: 25197 1.63 - 1.82: 156 Bond restraints: 85410 Sorted by residual: bond pdb=" O5' ADP F1101 " pdb=" PA ADP F1101 " ideal model delta sigma weight residual 1.610 1.807 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" O5' ADP G1101 " pdb=" PA ADP G1101 " ideal model delta sigma weight residual 1.610 1.804 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sigma weight residual 1.610 1.798 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " ideal model delta sigma weight residual 1.610 1.797 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" O3A ADP G1101 " pdb=" PB ADP G1101 " ideal model delta sigma weight residual 1.610 1.743 -0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 85405 not shown) Histogram of bond angle deviations from ideal: 76.33 - 87.88: 2 87.88 - 99.42: 19 99.42 - 110.96: 92387 110.96 - 122.50: 50498 122.50 - 134.04: 11444 Bond angle restraints: 154350 Sorted by residual: angle pdb=" H1 MET N 1 " pdb=" N MET N 1 " pdb=" H2 MET N 1 " ideal model delta sigma weight residual 109.47 76.33 33.14 3.00e+00 1.11e-01 1.22e+02 angle pdb=" H1 MET M 1 " pdb=" N MET M 1 " pdb=" H2 MET M 1 " ideal model delta sigma weight residual 109.47 86.08 23.39 3.00e+00 1.11e-01 6.08e+01 angle pdb=" H1 MET N 1 " pdb=" N MET N 1 " pdb=" H3 MET N 1 " ideal model delta sigma weight residual 109.47 130.92 -21.45 3.00e+00 1.11e-01 5.11e+01 angle pdb=" H1 MET M 1 " pdb=" N MET M 1 " pdb=" H3 MET M 1 " ideal model delta sigma weight residual 109.47 125.08 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C1' ADP F1101 " pdb=" C2' ADP F1101 " pdb=" C3' ADP F1101 " ideal model delta sigma weight residual 111.00 97.06 13.94 3.00e+00 1.11e-01 2.16e+01 ... (remaining 154345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.56: 36705 30.56 - 61.12: 2383 61.12 - 91.69: 121 91.69 - 122.25: 4 122.25 - 152.81: 3 Dihedral angle restraints: 39216 sinusoidal: 22896 harmonic: 16320 Sorted by residual: dihedral pdb=" C5' ADP G1101 " pdb=" O5' ADP G1101 " pdb=" PA ADP G1101 " pdb=" O2A ADP G1101 " ideal model delta sinusoidal sigma weight residual -60.00 92.81 -152.81 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" CA ASN C 126 " pdb=" C ASN C 126 " pdb=" N LEU C 127 " pdb=" CA LEU C 127 " ideal model delta harmonic sigma weight residual -180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" C5' ADP B1101 " pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " pdb=" O2A ADP B1101 " ideal model delta sinusoidal sigma weight residual -60.00 80.40 -140.40 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 39213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5939 0.058 - 0.116: 764 0.116 - 0.173: 50 0.173 - 0.231: 9 0.231 - 0.289: 4 Chirality restraints: 6766 Sorted by residual: chirality pdb=" C2' ADP G1101 " pdb=" C1' ADP G1101 " pdb=" C3' ADP G1101 " pdb=" O2' ADP G1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ADP A1101 " pdb=" C1' ADP A1101 " pdb=" C3' ADP A1101 " pdb=" O2' ADP A1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' ADP B1101 " pdb=" C1' ADP B1101 " pdb=" C3' ADP B1101 " pdb=" O2' ADP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 6763 not shown) Planarity restraints: 12186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 85 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO H 86 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 86 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 86 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 76 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO C 77 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 85 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO C 86 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.028 5.00e-02 4.00e+02 ... (remaining 12183 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 2123 2.10 - 2.72: 143726 2.72 - 3.35: 247244 3.35 - 3.97: 298161 3.97 - 4.60: 468695 Nonbonded interactions: 1159949 Sorted by model distance: nonbonded pdb=" OD1 ASN D 126 " pdb=" H GLN D 129 " model vdw 1.473 1.850 nonbonded pdb=" H LEU D 125 " pdb=" O ARG E 373 " model vdw 1.518 1.850 nonbonded pdb=" OD1 ASN F 183 " pdb=" H GLN F 186 " model vdw 1.535 1.850 nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLN A 186 " model vdw 1.548 1.850 nonbonded pdb="HH22 ARG E 128 " pdb=" OD2 ASP J 198 " model vdw 1.549 1.850 ... (remaining 1159944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 790 or (resid 791 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 792 through 1095 or resid 1101)) selection = chain 'B' selection = (chain 'F' and (resid 1 through 790 or (resid 791 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 792 through 1095 or resid 1101)) selection = chain 'G' } ncs_group { reference = (chain 'C' and (resid 40 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 140 through 234)) selection = chain 'D' selection = (chain 'H' and (resid 40 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 140 through 234)) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.880 Extract box with map and model: 9.900 Check model and map are aligned: 0.920 Set scattering table: 0.590 Process input model: 237.720 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 44058 Z= 0.228 Angle : 0.655 13.944 60300 Z= 0.359 Chirality : 0.038 0.289 6766 Planarity : 0.004 0.051 7330 Dihedral : 18.068 152.810 17210 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 4910 helix: 1.01 (0.10), residues: 2824 sheet: -1.78 (0.22), residues: 558 loop : -1.32 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 292 HIS 0.007 0.001 HIS A 862 PHE 0.010 0.001 PHE F 242 TYR 0.026 0.002 TYR A1089 ARG 0.008 0.000 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1077 MET cc_start: 0.9207 (ptp) cc_final: 0.8796 (ptt) REVERT: B 1 MET cc_start: 0.3243 (mtm) cc_final: 0.2979 (mtm) REVERT: B 171 MET cc_start: 0.8552 (ptm) cc_final: 0.8292 (ptm) REVERT: B 967 MET cc_start: 0.7827 (mmm) cc_final: 0.7237 (mmm) REVERT: E 335 PHE cc_start: 0.8833 (t80) cc_final: 0.8610 (t80) REVERT: G 967 MET cc_start: 0.7847 (mmm) cc_final: 0.7197 (mmm) REVERT: J 317 MET cc_start: 0.8854 (mmp) cc_final: 0.8531 (mmp) REVERT: J 335 PHE cc_start: 0.9018 (t80) cc_final: 0.8815 (t80) REVERT: M 1 MET cc_start: 0.6867 (mpp) cc_final: 0.6574 (mpp) REVERT: N 1 MET cc_start: 0.4096 (mmt) cc_final: 0.3802 (mmt) REVERT: N 23 GLU cc_start: 0.8051 (pt0) cc_final: 0.7621 (pt0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 1.2419 time to fit residues: 387.9654 Evaluate side-chains 161 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 427 optimal weight: 2.9990 chunk 383 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 258 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 396 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 241 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 459 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN J 80 GLN J 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 44058 Z= 0.231 Angle : 0.576 8.080 60300 Z= 0.326 Chirality : 0.038 0.169 6766 Planarity : 0.005 0.049 7330 Dihedral : 18.529 158.238 7382 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4910 helix: 0.66 (0.10), residues: 2856 sheet: -1.71 (0.22), residues: 546 loop : -1.42 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 15 HIS 0.007 0.001 HIS G1069 PHE 0.013 0.001 PHE E 247 TYR 0.019 0.002 TYR A1089 ARG 0.005 0.000 ARG B 939 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3344 (mtm) cc_final: 0.3058 (mtm) REVERT: B 171 MET cc_start: 0.8538 (ptm) cc_final: 0.8273 (ptm) REVERT: B 967 MET cc_start: 0.8054 (mmm) cc_final: 0.7499 (mmm) REVERT: E 401 PHE cc_start: 0.9031 (t80) cc_final: 0.8708 (t80) REVERT: G 967 MET cc_start: 0.8131 (mmm) cc_final: 0.7563 (mmm) REVERT: J 1 MET cc_start: 0.7627 (tmm) cc_final: 0.7046 (tmm) REVERT: J 335 PHE cc_start: 0.9124 (t80) cc_final: 0.8882 (t80) REVERT: J 401 PHE cc_start: 0.9197 (t80) cc_final: 0.8957 (t80) REVERT: M 1 MET cc_start: 0.6983 (mpp) cc_final: 0.6648 (mpp) REVERT: N 6 GLU cc_start: 0.8230 (mp0) cc_final: 0.8023 (mp0) REVERT: N 23 GLU cc_start: 0.7766 (pt0) cc_final: 0.7323 (pt0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 1.2048 time to fit residues: 367.1493 Evaluate side-chains 165 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 4.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 255 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 312 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 460 optimal weight: 5.9990 chunk 497 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 456 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 369 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 HIS ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 973 ASN ** F1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 44058 Z= 0.362 Angle : 0.650 8.409 60300 Z= 0.367 Chirality : 0.040 0.187 6766 Planarity : 0.005 0.054 7330 Dihedral : 18.311 171.196 7382 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.14 % Rotamer: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4910 helix: 0.17 (0.10), residues: 2836 sheet: -2.01 (0.21), residues: 558 loop : -1.83 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 15 HIS 0.012 0.002 HIS G1069 PHE 0.019 0.002 PHE J 247 TYR 0.023 0.002 TYR A 995 ARG 0.010 0.001 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3581 (mtm) cc_final: 0.3114 (mtm) REVERT: B 171 MET cc_start: 0.8573 (ptm) cc_final: 0.8280 (ptm) REVERT: B 967 MET cc_start: 0.7984 (mmm) cc_final: 0.7611 (mmm) REVERT: E 335 PHE cc_start: 0.8952 (t80) cc_final: 0.8747 (t80) REVERT: G 967 MET cc_start: 0.8264 (mmm) cc_final: 0.7883 (mmm) REVERT: J 1 MET cc_start: 0.7684 (tmm) cc_final: 0.7100 (tmm) REVERT: J 335 PHE cc_start: 0.9161 (t80) cc_final: 0.8921 (t80) REVERT: N 23 GLU cc_start: 0.7572 (pt0) cc_final: 0.7031 (pt0) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 1.1350 time to fit residues: 356.3959 Evaluate side-chains 161 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 454 optimal weight: 0.0270 chunk 346 optimal weight: 20.0000 chunk 238 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 219 optimal weight: 0.0060 chunk 309 optimal weight: 20.0000 chunk 461 optimal weight: 0.8980 chunk 489 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 437 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 153 GLN ** G 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN J 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 44058 Z= 0.147 Angle : 0.528 9.030 60300 Z= 0.295 Chirality : 0.036 0.160 6766 Planarity : 0.004 0.046 7330 Dihedral : 17.987 169.917 7382 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 4910 helix: 0.77 (0.10), residues: 2840 sheet: -1.96 (0.21), residues: 528 loop : -1.40 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP E 449 HIS 0.006 0.001 HIS F 791 PHE 0.009 0.001 PHE E 401 TYR 0.017 0.001 TYR E 70 ARG 0.006 0.000 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3469 (mtm) cc_final: 0.3056 (mtm) REVERT: B 967 MET cc_start: 0.7802 (mmm) cc_final: 0.7527 (mmm) REVERT: E 335 PHE cc_start: 0.8811 (t80) cc_final: 0.8604 (t80) REVERT: E 401 PHE cc_start: 0.9077 (t80) cc_final: 0.8762 (t80) REVERT: E 493 MET cc_start: 0.8112 (ptt) cc_final: 0.7570 (ptt) REVERT: G 139 MET cc_start: 0.8461 (ttp) cc_final: 0.8233 (tpp) REVERT: G 171 MET cc_start: 0.8532 (ptm) cc_final: 0.8327 (ptm) REVERT: G 967 MET cc_start: 0.8131 (mmm) cc_final: 0.7830 (mmm) REVERT: J 1 MET cc_start: 0.8177 (tmm) cc_final: 0.7642 (tmm) REVERT: J 310 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7803 (tt0) REVERT: J 335 PHE cc_start: 0.9050 (t80) cc_final: 0.8810 (t80) REVERT: J 401 PHE cc_start: 0.9201 (t80) cc_final: 0.8953 (t80) REVERT: N 23 GLU cc_start: 0.7565 (pt0) cc_final: 0.7101 (pt0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 1.1492 time to fit residues: 369.4724 Evaluate side-chains 159 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 407 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 417 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 439 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 865 HIS ** G 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44058 Z= 0.286 Angle : 0.585 8.573 60300 Z= 0.329 Chirality : 0.038 0.160 6766 Planarity : 0.004 0.052 7330 Dihedral : 17.909 168.515 7382 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.43 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4910 helix: 0.52 (0.10), residues: 2850 sheet: -2.09 (0.21), residues: 544 loop : -1.60 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 449 HIS 0.010 0.001 HIS A 865 PHE 0.017 0.001 PHE E 247 TYR 0.022 0.002 TYR A 995 ARG 0.005 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3614 (mtm) cc_final: 0.3143 (mtm) REVERT: B 171 MET cc_start: 0.8565 (ptm) cc_final: 0.8293 (ptm) REVERT: G 967 MET cc_start: 0.8162 (mmm) cc_final: 0.7867 (mmm) REVERT: J 1 MET cc_start: 0.8276 (tmm) cc_final: 0.7729 (tmm) REVERT: J 335 PHE cc_start: 0.9149 (t80) cc_final: 0.8947 (t80) REVERT: M 1 MET cc_start: 0.6948 (mpp) cc_final: 0.6613 (mpp) REVERT: N 23 GLU cc_start: 0.7563 (pt0) cc_final: 0.7126 (pt0) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 1.1549 time to fit residues: 346.9741 Evaluate side-chains 150 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 4.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 164 optimal weight: 6.9990 chunk 440 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 287 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 489 optimal weight: 2.9990 chunk 406 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44058 Z= 0.225 Angle : 0.552 8.927 60300 Z= 0.310 Chirality : 0.037 0.161 6766 Planarity : 0.004 0.046 7330 Dihedral : 17.799 166.886 7382 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.23 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4910 helix: 0.65 (0.10), residues: 2848 sheet: -2.00 (0.21), residues: 520 loop : -1.50 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 15 HIS 0.008 0.001 HIS A 862 PHE 0.013 0.001 PHE G 129 TYR 0.015 0.001 TYR A 995 ARG 0.006 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3606 (mtm) cc_final: 0.3141 (mtm) REVERT: B 171 MET cc_start: 0.8599 (ptm) cc_final: 0.8312 (ptm) REVERT: B 745 MET cc_start: 0.2407 (mtt) cc_final: 0.2144 (mtt) REVERT: B 967 MET cc_start: 0.7851 (mmm) cc_final: 0.7478 (mmm) REVERT: G 967 MET cc_start: 0.8141 (mmm) cc_final: 0.7798 (mmm) REVERT: J 1 MET cc_start: 0.8282 (tmm) cc_final: 0.8079 (tmm) REVERT: M 1 MET cc_start: 0.6918 (mpp) cc_final: 0.6603 (mpp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 1.1486 time to fit residues: 343.9616 Evaluate side-chains 151 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 472 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 487 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 164 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44058 Z= 0.283 Angle : 0.581 8.286 60300 Z= 0.327 Chirality : 0.038 0.154 6766 Planarity : 0.004 0.061 7330 Dihedral : 17.776 159.309 7382 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 4910 helix: 0.51 (0.10), residues: 2858 sheet: -2.11 (0.21), residues: 536 loop : -1.62 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP E 449 HIS 0.008 0.001 HIS B1069 PHE 0.015 0.001 PHE J 247 TYR 0.019 0.002 TYR A 995 ARG 0.006 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1077 MET cc_start: 0.9104 (ptp) cc_final: 0.8681 (ptt) REVERT: B 1 MET cc_start: 0.3625 (mtm) cc_final: 0.3131 (mtm) REVERT: B 171 MET cc_start: 0.8611 (ptm) cc_final: 0.8313 (ptm) REVERT: B 745 MET cc_start: 0.2666 (mtt) cc_final: 0.2329 (mtt) REVERT: B 967 MET cc_start: 0.7810 (mmm) cc_final: 0.7452 (mmm) REVERT: G 171 MET cc_start: 0.8565 (ptm) cc_final: 0.8262 (ptm) REVERT: G 967 MET cc_start: 0.8114 (mmm) cc_final: 0.7775 (mmm) REVERT: J 1 MET cc_start: 0.8343 (tmm) cc_final: 0.8113 (tmm) REVERT: M 1 MET cc_start: 0.7023 (mpp) cc_final: 0.6714 (mpp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.1251 time to fit residues: 340.3449 Evaluate side-chains 148 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 301 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 310 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G 973 ASN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44058 Z= 0.254 Angle : 0.566 7.599 60300 Z= 0.318 Chirality : 0.038 0.155 6766 Planarity : 0.004 0.078 7330 Dihedral : 17.730 159.463 7382 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.97 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4910 helix: 0.57 (0.10), residues: 2858 sheet: -2.10 (0.21), residues: 536 loop : -1.57 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 449 HIS 0.008 0.001 HIS F 862 PHE 0.013 0.001 PHE J 247 TYR 0.017 0.002 TYR A 995 ARG 0.005 0.000 ARG B 939 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3664 (mtm) cc_final: 0.3163 (mtm) REVERT: B 171 MET cc_start: 0.8630 (ptm) cc_final: 0.8327 (ptm) REVERT: B 745 MET cc_start: 0.2639 (mtt) cc_final: 0.2239 (mtt) REVERT: B 967 MET cc_start: 0.7961 (mmm) cc_final: 0.7491 (mmm) REVERT: G 967 MET cc_start: 0.8061 (mmm) cc_final: 0.7824 (mmm) REVERT: J 1 MET cc_start: 0.8401 (tmm) cc_final: 0.8167 (tmm) REVERT: M 1 MET cc_start: 0.7014 (mpp) cc_final: 0.6719 (mpp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 1.1461 time to fit residues: 350.4829 Evaluate side-chains 151 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 443 optimal weight: 1.9990 chunk 467 optimal weight: 3.9990 chunk 426 optimal weight: 0.9980 chunk 454 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 410 optimal weight: 10.0000 chunk 429 optimal weight: 0.5980 chunk 452 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN J 144 ASN J 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44058 Z= 0.174 Angle : 0.525 6.867 60300 Z= 0.293 Chirality : 0.036 0.153 6766 Planarity : 0.004 0.056 7330 Dihedral : 17.587 160.163 7382 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4910 helix: 0.85 (0.10), residues: 2848 sheet: -1.92 (0.22), residues: 518 loop : -1.45 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 449 HIS 0.007 0.001 HIS D 139 PHE 0.011 0.001 PHE E 401 TYR 0.012 0.001 TYR F1089 ARG 0.006 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3617 (mtm) cc_final: 0.3114 (mtm) REVERT: B 139 MET cc_start: 0.7530 (tpp) cc_final: 0.7108 (tpp) REVERT: B 171 MET cc_start: 0.8641 (ptm) cc_final: 0.8337 (ptm) REVERT: B 967 MET cc_start: 0.8048 (mmm) cc_final: 0.7826 (mmm) REVERT: G 171 MET cc_start: 0.8578 (ptm) cc_final: 0.8282 (ptm) REVERT: J 1 MET cc_start: 0.8487 (tmm) cc_final: 0.8273 (tmm) REVERT: N 19 LYS cc_start: 0.7638 (tppt) cc_final: 0.7422 (tppt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 1.1657 time to fit residues: 365.2433 Evaluate side-chains 155 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 4.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 298 optimal weight: 2.9990 chunk 480 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 504 optimal weight: 10.0000 chunk 463 optimal weight: 4.9990 chunk 401 optimal weight: 0.0270 chunk 41 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 HIS ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1029 HIS ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN M 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44058 Z= 0.231 Angle : 0.547 7.364 60300 Z= 0.306 Chirality : 0.037 0.149 6766 Planarity : 0.004 0.049 7330 Dihedral : 17.541 159.421 7382 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.88 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4910 helix: 0.77 (0.10), residues: 2856 sheet: -1.79 (0.21), residues: 552 loop : -1.60 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 449 HIS 0.008 0.001 HIS A 862 PHE 0.012 0.001 PHE J 247 TYR 0.016 0.001 TYR A 995 ARG 0.006 0.000 ARG E 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9820 Ramachandran restraints generated. 4910 Oldfield, 0 Emsley, 4910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3585 (mtm) cc_final: 0.3106 (mtm) REVERT: B 171 MET cc_start: 0.8644 (ptm) cc_final: 0.8337 (ptm) REVERT: G 171 MET cc_start: 0.8578 (ptm) cc_final: 0.8280 (ptm) REVERT: J 1 MET cc_start: 0.8523 (tmm) cc_final: 0.8306 (tmm) REVERT: M 1 MET cc_start: 0.7184 (mpp) cc_final: 0.6933 (mpp) REVERT: N 19 LYS cc_start: 0.7712 (tppt) cc_final: 0.7484 (tppt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 1.1781 time to fit residues: 359.4314 Evaluate side-chains 151 residues out of total 4246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 318 optimal weight: 3.9990 chunk 427 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 402 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 412 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.106251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075208 restraints weight = 546038.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.076529 restraints weight = 314152.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076204 restraints weight = 220770.106| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 44058 Z= 0.233 Angle : 0.548 8.066 60300 Z= 0.306 Chirality : 0.037 0.151 6766 Planarity : 0.004 0.051 7330 Dihedral : 17.507 159.674 7382 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.80 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4910 helix: 0.76 (0.10), residues: 2860 sheet: -1.85 (0.21), residues: 560 loop : -1.61 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 449 HIS 0.008 0.001 HIS A 862 PHE 0.012 0.001 PHE J 247 TYR 0.016 0.001 TYR A 995 ARG 0.008 0.000 ARG E 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10591.21 seconds wall clock time: 186 minutes 11.35 seconds (11171.35 seconds total)