Starting phenix.real_space_refine on Tue Aug 26 21:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s70_19761/08_2025/8s70_19761.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 112 5.49 5 Mg 16 5.21 5 S 160 5.16 5 C 25456 2.51 5 N 7136 2.21 5 O 8240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41120 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, F, H, J, L, N, P, R, U, W, Y, D, 0, 2, 4, E, G, I, K, M, O, Q, S, V, X, Z, T, 1, 3, 5 Time building chain proxies: 3.65, per 1000 atoms: 0.09 Number of scatterers: 41120 At special positions: 0 Unit cell: (127.358, 119.915, 321.703, 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 160 16.00 P 112 15.00 Mg 16 11.99 O 8240 8.00 N 7136 7.00 C 25456 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=45, symmetry=0 Number of additional bonds: simple=45, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 476.8 nanoseconds 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9280 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 45.7% alpha, 15.2% beta 0 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'D' and resid 1 through 21 Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 21 Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 165 through 185 removed outlier: 3.551A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 21 Processing helix chain 'C' and resid 22 through 25 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP C 310 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 21 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 150 through 156 Processing helix chain 'F' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 218 removed outlier: 3.830A pdb=" N PHE F 216 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP F 310 " --> pdb=" O LYS F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 21 Processing helix chain 'H' and resid 22 through 25 Processing helix chain 'H' and resid 43 through 50 Processing helix chain 'H' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU H 76 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 120 through 135 Processing helix chain 'H' and resid 150 through 156 Processing helix chain 'H' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY H 179 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE H 216 " --> pdb=" O ASN H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR H 321 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE H 322 " --> pdb=" O LEU H 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 21 Processing helix chain 'J' and resid 22 through 25 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 106 Processing helix chain 'J' and resid 120 through 135 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU J 169 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE J 216 " --> pdb=" O ASN J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP J 310 " --> pdb=" O LYS J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR J 321 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE J 322 " --> pdb=" O LEU J 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 21 Processing helix chain 'L' and resid 22 through 25 Processing helix chain 'L' and resid 43 through 50 Processing helix chain 'L' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 106 Processing helix chain 'L' and resid 120 through 135 Processing helix chain 'L' and resid 150 through 156 Processing helix chain 'L' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU L 169 " --> pdb=" O LEU L 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY L 179 " --> pdb=" O ARG L 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN L 180 " --> pdb=" O LYS L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP L 310 " --> pdb=" O LYS L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR L 321 " --> pdb=" O VAL L 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 322 " --> pdb=" O LEU L 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 21 Processing helix chain 'N' and resid 22 through 25 Processing helix chain 'N' and resid 43 through 50 Processing helix chain 'N' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU N 76 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 77 " --> pdb=" O THR N 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL N 78 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 106 Processing helix chain 'N' and resid 120 through 135 Processing helix chain 'N' and resid 150 through 156 Processing helix chain 'N' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU N 169 " --> pdb=" O LEU N 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY N 179 " --> pdb=" O ARG N 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN N 180 " --> pdb=" O LYS N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE N 216 " --> pdb=" O ASN N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP N 310 " --> pdb=" O LYS N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR N 321 " --> pdb=" O VAL N 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE N 322 " --> pdb=" O LEU N 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 21 Processing helix chain 'P' and resid 22 through 25 Processing helix chain 'P' and resid 43 through 50 Processing helix chain 'P' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU P 76 " --> pdb=" O THR P 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER P 77 " --> pdb=" O THR P 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL P 78 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 106 Processing helix chain 'P' and resid 120 through 135 Processing helix chain 'P' and resid 150 through 156 Processing helix chain 'P' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN P 180 " --> pdb=" O LYS P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE P 216 " --> pdb=" O ASN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU P 272 " --> pdb=" O TYR P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP P 310 " --> pdb=" O LYS P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE P 322 " --> pdb=" O LEU P 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 21 Processing helix chain 'R' and resid 22 through 25 Processing helix chain 'R' and resid 43 through 50 Processing helix chain 'R' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 106 Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 150 through 156 Processing helix chain 'R' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY R 179 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN R 180 " --> pdb=" O LYS R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE R 216 " --> pdb=" O ASN R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP R 310 " --> pdb=" O LYS R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) Processing helix chain 'U' and resid 1 through 21 Processing helix chain 'U' and resid 22 through 25 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'U' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU U 76 " --> pdb=" O THR U 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER U 77 " --> pdb=" O THR U 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 106 Processing helix chain 'U' and resid 120 through 135 Processing helix chain 'U' and resid 150 through 156 Processing helix chain 'U' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU U 169 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN U 180 " --> pdb=" O LYS U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE U 216 " --> pdb=" O ASN U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU U 272 " --> pdb=" O TYR U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP U 310 " --> pdb=" O LYS U 306 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR U 321 " --> pdb=" O VAL U 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE U 322 " --> pdb=" O LEU U 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 1 through 21 Processing helix chain 'W' and resid 22 through 25 Processing helix chain 'W' and resid 43 through 50 Processing helix chain 'W' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU W 76 " --> pdb=" O THR W 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER W 77 " --> pdb=" O THR W 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL W 78 " --> pdb=" O LEU W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 106 Processing helix chain 'W' and resid 120 through 135 Processing helix chain 'W' and resid 150 through 156 Processing helix chain 'W' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU W 169 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY W 179 " --> pdb=" O ARG W 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN W 180 " --> pdb=" O LYS W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE W 216 " --> pdb=" O ASN W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU W 272 " --> pdb=" O TYR W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP W 310 " --> pdb=" O LYS W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR W 321 " --> pdb=" O VAL W 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE W 322 " --> pdb=" O LEU W 318 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 21 Processing helix chain 'Y' and resid 22 through 25 Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Y' and resid 70 through 86 removed outlier: 3.673A pdb=" N LEU Y 76 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER Y 77 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL Y 78 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 106 Processing helix chain 'Y' and resid 120 through 135 Processing helix chain 'Y' and resid 150 through 156 Processing helix chain 'Y' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU Y 169 " --> pdb=" O LEU Y 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY Y 179 " --> pdb=" O ARG Y 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN Y 180 " --> pdb=" O LYS Y 176 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE Y 216 " --> pdb=" O ASN Y 212 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR Y 321 " --> pdb=" O VAL Y 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Y 322 " --> pdb=" O LEU Y 318 " (cutoff:3.500A) Processing helix chain '0' and resid 1 through 21 Processing helix chain '0' and resid 22 through 25 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 0 76 " --> pdb=" O THR 0 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 0 77 " --> pdb=" O THR 0 73 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL 0 78 " --> pdb=" O LEU 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 99 through 106 Processing helix chain '0' and resid 120 through 135 Processing helix chain '0' and resid 150 through 156 Processing helix chain '0' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU 0 169 " --> pdb=" O LEU 0 165 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY 0 179 " --> pdb=" O ARG 0 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN 0 180 " --> pdb=" O LYS 0 176 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 218 removed outlier: 3.832A pdb=" N PHE 0 216 " --> pdb=" O ASN 0 212 " (cutoff:3.500A) Processing helix chain '0' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU 0 272 " --> pdb=" O TYR 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 0 310 " --> pdb=" O LYS 0 306 " (cutoff:3.500A) Processing helix chain '0' and resid 311 through 327 removed outlier: 3.586A pdb=" N THR 0 321 " --> pdb=" O VAL 0 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 0 322 " --> pdb=" O LEU 0 318 " (cutoff:3.500A) Processing helix chain '2' and resid 1 through 21 Processing helix chain '2' and resid 22 through 25 Processing helix chain '2' and resid 43 through 50 Processing helix chain '2' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 2 76 " --> pdb=" O THR 2 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 2 77 " --> pdb=" O THR 2 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 2 78 " --> pdb=" O LEU 2 74 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 106 Processing helix chain '2' and resid 120 through 135 Processing helix chain '2' and resid 150 through 156 Processing helix chain '2' and resid 165 through 185 removed outlier: 3.551A pdb=" N LEU 2 169 " --> pdb=" O LEU 2 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY 2 179 " --> pdb=" O ARG 2 175 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN 2 180 " --> pdb=" O LYS 2 176 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE 2 216 " --> pdb=" O ASN 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 280 removed outlier: 3.526A pdb=" N GLU 2 272 " --> pdb=" O TYR 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 2 310 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR 2 321 " --> pdb=" O VAL 2 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 2 322 " --> pdb=" O LEU 2 318 " (cutoff:3.500A) Processing helix chain '4' and resid 1 through 21 Processing helix chain '4' and resid 22 through 25 Processing helix chain '4' and resid 43 through 50 Processing helix chain '4' and resid 70 through 86 removed outlier: 3.672A pdb=" N LEU 4 76 " --> pdb=" O THR 4 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER 4 77 " --> pdb=" O THR 4 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 106 Processing helix chain '4' and resid 120 through 135 Processing helix chain '4' and resid 150 through 156 Processing helix chain '4' and resid 165 through 185 removed outlier: 3.552A pdb=" N LEU 4 169 " --> pdb=" O LEU 4 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY 4 179 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN 4 180 " --> pdb=" O LYS 4 176 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 removed outlier: 3.831A pdb=" N PHE 4 216 " --> pdb=" O ASN 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 280 removed outlier: 3.527A pdb=" N GLU 4 272 " --> pdb=" O TYR 4 268 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 310 removed outlier: 3.542A pdb=" N ASP 4 310 " --> pdb=" O LYS 4 306 " (cutoff:3.500A) Processing helix chain '4' and resid 311 through 327 removed outlier: 3.587A pdb=" N THR 4 321 " --> pdb=" O VAL 4 317 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 4 322 " --> pdb=" O LEU 4 318 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=2, first strand: chain 'D' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL D 142 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 191 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 60 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU D 222 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 62 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 224 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 64 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG D 226 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 227 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU D 240 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA D 229 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY D 238 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS D 231 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 236 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 285 through 286 Processing sheet with id=4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=5, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.745A pdb=" N VAL A 142 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 191 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 60 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU A 222 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU A 62 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 224 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 64 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG A 226 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 227 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU A 240 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA A 229 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 238 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 231 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 236 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=8, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL C 142 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 191 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 60 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU C 222 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU C 62 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE C 224 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 64 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG C 226 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 227 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU C 240 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA C 229 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 238 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS C 231 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 236 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=10, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=11, first strand: chain 'F' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL F 142 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 191 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 60 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU F 222 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU F 62 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 224 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR F 64 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG F 226 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG F 221 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR F 227 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU F 240 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA F 229 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY F 238 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS F 231 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 236 " --> pdb=" O LYS F 231 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 285 through 286 Processing sheet with id=13, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=14, first strand: chain 'H' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL H 142 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 191 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE H 60 " --> pdb=" O VAL H 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU H 222 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU H 62 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE H 224 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 64 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG H 226 " --> pdb=" O TYR H 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 221 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR H 227 " --> pdb=" O GLU H 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU H 240 " --> pdb=" O THR H 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA H 229 " --> pdb=" O GLY H 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY H 238 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS H 231 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 236 " --> pdb=" O LYS H 231 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 285 through 286 Processing sheet with id=16, first strand: chain 'J' and resid 38 through 39 Processing sheet with id=17, first strand: chain 'J' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL J 142 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE J 191 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE J 60 " --> pdb=" O VAL J 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU J 222 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU J 62 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE J 224 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR J 64 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG J 226 " --> pdb=" O TYR J 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG J 221 " --> pdb=" O VAL J 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR J 227 " --> pdb=" O GLU J 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU J 240 " --> pdb=" O THR J 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA J 229 " --> pdb=" O GLY J 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY J 238 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS J 231 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL J 236 " --> pdb=" O LYS J 231 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'J' and resid 285 through 286 Processing sheet with id=19, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=20, first strand: chain 'L' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL L 142 " --> pdb=" O ILE L 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE L 191 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 60 " --> pdb=" O VAL L 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU L 222 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU L 62 " --> pdb=" O LEU L 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE L 224 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR L 64 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG L 226 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG L 221 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR L 227 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU L 240 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA L 229 " --> pdb=" O GLY L 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY L 238 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS L 231 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL L 236 " --> pdb=" O LYS L 231 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'L' and resid 285 through 286 Processing sheet with id=22, first strand: chain 'N' and resid 38 through 39 Processing sheet with id=23, first strand: chain 'N' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL N 142 " --> pdb=" O ILE N 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE N 191 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE N 60 " --> pdb=" O VAL N 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU N 222 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU N 62 " --> pdb=" O LEU N 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE N 224 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR N 64 " --> pdb=" O ILE N 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG N 226 " --> pdb=" O TYR N 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG N 221 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR N 227 " --> pdb=" O GLU N 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU N 240 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA N 229 " --> pdb=" O GLY N 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY N 238 " --> pdb=" O ALA N 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS N 231 " --> pdb=" O VAL N 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL N 236 " --> pdb=" O LYS N 231 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'N' and resid 285 through 286 Processing sheet with id=25, first strand: chain 'P' and resid 38 through 39 Processing sheet with id=26, first strand: chain 'P' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL P 142 " --> pdb=" O ILE P 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE P 191 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE P 60 " --> pdb=" O VAL P 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU P 222 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU P 62 " --> pdb=" O LEU P 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE P 224 " --> pdb=" O GLU P 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR P 64 " --> pdb=" O ILE P 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG P 226 " --> pdb=" O TYR P 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG P 221 " --> pdb=" O VAL P 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR P 227 " --> pdb=" O GLU P 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU P 240 " --> pdb=" O THR P 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA P 229 " --> pdb=" O GLY P 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY P 238 " --> pdb=" O ALA P 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS P 231 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL P 236 " --> pdb=" O LYS P 231 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'P' and resid 285 through 286 Processing sheet with id=28, first strand: chain 'R' and resid 38 through 39 Processing sheet with id=29, first strand: chain 'R' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL R 142 " --> pdb=" O ILE R 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE R 191 " --> pdb=" O VAL R 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE R 60 " --> pdb=" O VAL R 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU R 222 " --> pdb=" O ILE R 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU R 62 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE R 224 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR R 64 " --> pdb=" O ILE R 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG R 226 " --> pdb=" O TYR R 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG R 221 " --> pdb=" O VAL R 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR R 227 " --> pdb=" O GLU R 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU R 240 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA R 229 " --> pdb=" O GLY R 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY R 238 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS R 231 " --> pdb=" O VAL R 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL R 236 " --> pdb=" O LYS R 231 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'R' and resid 285 through 286 Processing sheet with id=31, first strand: chain 'U' and resid 38 through 39 Processing sheet with id=32, first strand: chain 'U' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL U 142 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE U 191 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE U 60 " --> pdb=" O VAL U 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU U 222 " --> pdb=" O ILE U 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU U 62 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE U 224 " --> pdb=" O GLU U 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR U 64 " --> pdb=" O ILE U 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG U 226 " --> pdb=" O TYR U 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG U 221 " --> pdb=" O VAL U 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR U 227 " --> pdb=" O GLU U 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU U 240 " --> pdb=" O THR U 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA U 229 " --> pdb=" O GLY U 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY U 238 " --> pdb=" O ALA U 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS U 231 " --> pdb=" O VAL U 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL U 236 " --> pdb=" O LYS U 231 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'U' and resid 285 through 286 Processing sheet with id=34, first strand: chain 'W' and resid 38 through 39 Processing sheet with id=35, first strand: chain 'W' and resid 89 through 93 removed outlier: 3.745A pdb=" N VAL W 142 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE W 191 " --> pdb=" O VAL W 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE W 60 " --> pdb=" O VAL W 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU W 222 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU W 62 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE W 224 " --> pdb=" O GLU W 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR W 64 " --> pdb=" O ILE W 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG W 226 " --> pdb=" O TYR W 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG W 221 " --> pdb=" O VAL W 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR W 227 " --> pdb=" O GLU W 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU W 240 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA W 229 " --> pdb=" O GLY W 238 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY W 238 " --> pdb=" O ALA W 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS W 231 " --> pdb=" O VAL W 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL W 236 " --> pdb=" O LYS W 231 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'W' and resid 285 through 286 Processing sheet with id=37, first strand: chain 'Y' and resid 38 through 39 Processing sheet with id=38, first strand: chain 'Y' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL Y 142 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Y 191 " --> pdb=" O VAL Y 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Y 60 " --> pdb=" O VAL Y 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU Y 222 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU Y 62 " --> pdb=" O LEU Y 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE Y 224 " --> pdb=" O GLU Y 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR Y 64 " --> pdb=" O ILE Y 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG Y 226 " --> pdb=" O TYR Y 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG Y 221 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR Y 227 " --> pdb=" O GLU Y 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU Y 240 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA Y 229 " --> pdb=" O GLY Y 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY Y 238 " --> pdb=" O ALA Y 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS Y 231 " --> pdb=" O VAL Y 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL Y 236 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'Y' and resid 285 through 286 Processing sheet with id=40, first strand: chain '0' and resid 38 through 39 Processing sheet with id=41, first strand: chain '0' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 0 142 " --> pdb=" O ILE 0 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 0 191 " --> pdb=" O VAL 0 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE 0 60 " --> pdb=" O VAL 0 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 0 222 " --> pdb=" O ILE 0 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 0 62 " --> pdb=" O LEU 0 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 0 224 " --> pdb=" O GLU 0 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 0 64 " --> pdb=" O ILE 0 224 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG 0 226 " --> pdb=" O TYR 0 64 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG 0 221 " --> pdb=" O VAL 0 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR 0 227 " --> pdb=" O GLU 0 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU 0 240 " --> pdb=" O THR 0 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA 0 229 " --> pdb=" O GLY 0 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY 0 238 " --> pdb=" O ALA 0 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS 0 231 " --> pdb=" O VAL 0 236 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL 0 236 " --> pdb=" O LYS 0 231 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain '0' and resid 285 through 286 Processing sheet with id=43, first strand: chain '2' and resid 38 through 39 Processing sheet with id=44, first strand: chain '2' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 2 191 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE 2 60 " --> pdb=" O VAL 2 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 2 222 " --> pdb=" O ILE 2 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 2 62 " --> pdb=" O LEU 2 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 2 224 " --> pdb=" O GLU 2 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 2 64 " --> pdb=" O ILE 2 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG 2 226 " --> pdb=" O TYR 2 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG 2 221 " --> pdb=" O VAL 2 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR 2 227 " --> pdb=" O GLU 2 240 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU 2 240 " --> pdb=" O THR 2 227 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA 2 229 " --> pdb=" O GLY 2 238 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY 2 238 " --> pdb=" O ALA 2 229 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS 2 231 " --> pdb=" O VAL 2 236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL 2 236 " --> pdb=" O LYS 2 231 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain '2' and resid 285 through 286 Processing sheet with id=46, first strand: chain '4' and resid 38 through 39 Processing sheet with id=47, first strand: chain '4' and resid 89 through 93 removed outlier: 3.746A pdb=" N VAL 4 142 " --> pdb=" O ILE 4 189 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE 4 191 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE 4 60 " --> pdb=" O VAL 4 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU 4 222 " --> pdb=" O ILE 4 60 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU 4 62 " --> pdb=" O LEU 4 222 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE 4 224 " --> pdb=" O GLU 4 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 4 64 " --> pdb=" O ILE 4 224 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ARG 4 226 " --> pdb=" O TYR 4 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG 4 221 " --> pdb=" O VAL 4 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR 4 227 " --> pdb=" O GLU 4 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU 4 240 " --> pdb=" O THR 4 227 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA 4 229 " --> pdb=" O GLY 4 238 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY 4 238 " --> pdb=" O ALA 4 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS 4 231 " --> pdb=" O VAL 4 236 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL 4 236 " --> pdb=" O LYS 4 231 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '4' and resid 285 through 286 1904 hydrogen bonds defined for protein. 5472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 13856 1.36 - 1.51: 10149 1.51 - 1.65: 17435 1.65 - 1.80: 128 1.80 - 1.95: 144 Bond restraints: 41712 Sorted by residual: bond pdb=" N VAL F 132 " pdb=" CA VAL F 132 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 6.02e+00 bond pdb=" N VAL N 132 " pdb=" CA VAL N 132 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 5.96e+00 bond pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 5.91e+00 bond pdb=" N VAL W 132 " pdb=" CA VAL W 132 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 5.90e+00 bond pdb=" N VAL C 132 " pdb=" CA VAL C 132 " ideal model delta sigma weight residual 1.461 1.489 -0.029 1.19e-02 7.06e+03 5.87e+00 ... (remaining 41707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 52997 1.07 - 2.14: 2574 2.14 - 3.21: 749 3.21 - 4.29: 144 4.29 - 5.36: 128 Bond angle restraints: 56592 Sorted by residual: angle pdb=" N ILE P 52 " pdb=" CA ILE P 52 " pdb=" C ILE P 52 " ideal model delta sigma weight residual 113.20 108.82 4.38 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N ILE F 52 " pdb=" CA ILE F 52 " pdb=" C ILE F 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N ILE R 52 " pdb=" CA ILE R 52 " pdb=" C ILE R 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.07e+01 angle pdb=" N ILE C 52 " pdb=" CA ILE C 52 " pdb=" C ILE C 52 " ideal model delta sigma weight residual 113.20 108.83 4.37 9.60e-01 1.09e+00 2.07e+01 angle pdb=" N ILE L 52 " pdb=" CA ILE L 52 " pdb=" C ILE L 52 " ideal model delta sigma weight residual 113.20 108.84 4.36 9.60e-01 1.09e+00 2.07e+01 ... (remaining 56587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 23120 17.74 - 35.47: 1408 35.47 - 53.21: 496 53.21 - 70.95: 96 70.95 - 88.68: 48 Dihedral angle restraints: 25168 sinusoidal: 10528 harmonic: 14640 Sorted by residual: dihedral pdb=" CB GLU 0 258 " pdb=" CG GLU 0 258 " pdb=" CD GLU 0 258 " pdb=" OE1 GLU 0 258 " ideal model delta sinusoidal sigma weight residual 0.00 -79.69 79.69 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU R 258 " pdb=" CG GLU R 258 " pdb=" CD GLU R 258 " pdb=" OE1 GLU R 258 " ideal model delta sinusoidal sigma weight residual 0.00 -79.69 79.69 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU C 258 " pdb=" CG GLU C 258 " pdb=" CD GLU C 258 " pdb=" OE1 GLU C 258 " ideal model delta sinusoidal sigma weight residual 0.00 -79.69 79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 25165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3864 0.030 - 0.060: 1532 0.060 - 0.091: 778 0.091 - 0.121: 262 0.121 - 0.151: 108 Chirality restraints: 6544 Sorted by residual: chirality pdb=" CB VAL 2 132 " pdb=" CA VAL 2 132 " pdb=" CG1 VAL 2 132 " pdb=" CG2 VAL 2 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB VAL L 132 " pdb=" CA VAL L 132 " pdb=" CG1 VAL L 132 " pdb=" CG2 VAL L 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CB VAL N 132 " pdb=" CA VAL N 132 " pdb=" CG1 VAL N 132 " pdb=" CG2 VAL N 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 6541 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 204 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO F 205 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN W 204 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO W 205 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO W 205 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO W 205 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 204 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO P 205 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO P 205 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 205 " 0.024 5.00e-02 4.00e+02 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 360 1.29 - 2.19: 1698 2.19 - 3.10: 35851 3.10 - 4.00: 113033 4.00 - 4.90: 191546 Warning: very small nonbonded interaction distances. Nonbonded interactions: 342488 Sorted by model distance: nonbonded pdb=" OG1 THR U 72 " pdb="MG MG W 401 " model vdw 0.390 2.170 nonbonded pdb=" OG1 THR N 72 " pdb="MG MG P 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR R 72 " pdb="MG MG U 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR F 72 " pdb="MG MG H 401 " model vdw 0.391 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG 0 401 " model vdw 0.391 2.170 ... (remaining 342483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'D' selection = chain '0' selection = chain '2' selection = chain '4' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'T' selection = chain '1' selection = chain '3' selection = chain '5' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.050 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 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 : 0.020 0.700 41757 Z= 1.961 Angle : 0.629 5.357 56592 Z= 0.361 Chirality : 0.044 0.151 6544 Planarity : 0.004 0.044 7120 Dihedral : 13.873 88.683 15888 Min Nonbonded Distance : 0.390 Molprobity Statistics. All-atom Clashscore : 45.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.12), residues: 5216 helix: 1.44 (0.11), residues: 2240 sheet: 1.42 (0.19), residues: 816 loop : -0.80 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.009 0.001 TYR W 268 PHE 0.010 0.002 PHE 0 259 TRP 0.004 0.001 TRP U 289 HIS 0.005 0.001 HIS 2 96 Details of bonding type rmsd covalent geometry : bond 0.00358 (41712) covalent geometry : angle 0.62879 (56592) hydrogen bonds : bond 0.19642 ( 1904) hydrogen bonds : angle 7.40824 ( 5472) Misc. bond : bond 0.59462 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 889 time to evaluate : 1.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 130 MET cc_start: 0.7550 (ttt) cc_final: 0.7294 (ttt) REVERT: A 180 ASN cc_start: 0.9016 (m-40) cc_final: 0.8260 (t0) REVERT: A 206 GLU cc_start: 0.8440 (mp0) cc_final: 0.8050 (mp0) REVERT: A 237 VAL cc_start: 0.8477 (p) cc_final: 0.7904 (p) REVERT: A 303 ASN cc_start: 0.9511 (m-40) cc_final: 0.9284 (t0) REVERT: C 98 LEU cc_start: 0.8815 (tp) cc_final: 0.8515 (pp) REVERT: C 130 MET cc_start: 0.8207 (ttt) cc_final: 0.6604 (ttt) REVERT: C 151 LYS cc_start: 0.9018 (ptmm) cc_final: 0.8586 (tppt) REVERT: C 201 MET cc_start: 0.6104 (pmm) cc_final: 0.5903 (pmm) REVERT: C 276 LEU cc_start: 0.8918 (mp) cc_final: 0.8673 (tp) REVERT: F 254 PHE cc_start: 0.5726 (m-80) cc_final: 0.5317 (m-10) REVERT: H 26 MET cc_start: 0.0118 (ptt) cc_final: -0.0428 (ptt) REVERT: H 242 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.7119 (mmm160) REVERT: J 74 LEU cc_start: 0.6794 (tp) cc_final: 0.6555 (mt) REVERT: J 236 VAL cc_start: 0.6928 (m) cc_final: 0.5720 (p) REVERT: L 64 TYR cc_start: 0.6291 (p90) cc_final: 0.6026 (p90) REVERT: L 254 PHE cc_start: 0.7691 (m-80) cc_final: 0.7207 (m-80) REVERT: N 26 MET cc_start: 0.0280 (ptt) cc_final: -0.0088 (pmm) REVERT: N 27 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7562 (mtt180) REVERT: N 130 MET cc_start: 0.7529 (ttt) cc_final: 0.7253 (ttt) REVERT: N 180 ASN cc_start: 0.9410 (m-40) cc_final: 0.8788 (t0) REVERT: N 206 GLU cc_start: 0.8922 (mp0) cc_final: 0.8518 (mp0) REVERT: N 244 LYS cc_start: 0.9400 (tttt) cc_final: 0.9186 (tppt) REVERT: N 290 TYR cc_start: 0.9255 (m-80) cc_final: 0.8668 (m-80) REVERT: P 26 MET cc_start: -0.1811 (ptt) cc_final: -0.2574 (pmm) REVERT: P 130 MET cc_start: 0.6934 (ttt) cc_final: 0.6718 (ttt) REVERT: P 222 LEU cc_start: 0.7075 (mp) cc_final: 0.6707 (mm) REVERT: P 276 LEU cc_start: 0.9323 (mp) cc_final: 0.9075 (tp) REVERT: P 303 ASN cc_start: 0.9106 (m-40) cc_final: 0.8705 (t0) REVERT: R 26 MET cc_start: -0.1354 (ptt) cc_final: -0.1558 (ptp) REVERT: U 26 MET cc_start: -0.0584 (ptt) cc_final: -0.1986 (pmm) REVERT: U 301 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6965 (mmtt) REVERT: W 92 VAL cc_start: 0.7745 (p) cc_final: 0.7352 (m) REVERT: Y 66 PRO cc_start: 0.6632 (Cg_exo) cc_final: 0.6352 (Cg_endo) REVERT: D 27 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7738 (mtm-85) REVERT: D 30 ASP cc_start: 0.8589 (t70) cc_final: 0.8015 (t0) REVERT: D 64 TYR cc_start: 0.8293 (p90) cc_final: 0.7663 (p90) REVERT: D 130 MET cc_start: 0.8577 (ttt) cc_final: 0.8269 (ttt) REVERT: D 151 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9044 (tppt) REVERT: D 180 ASN cc_start: 0.9403 (m-40) cc_final: 0.8977 (t0) REVERT: D 190 PHE cc_start: 0.8976 (m-80) cc_final: 0.8488 (m-10) REVERT: D 206 GLU cc_start: 0.8827 (mp0) cc_final: 0.8408 (mp0) REVERT: D 268 TYR cc_start: 0.8541 (t80) cc_final: 0.8193 (t80) REVERT: 0 26 MET cc_start: -0.0497 (ptt) cc_final: -0.0785 (pmm) REVERT: 0 81 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8711 (mm-30) REVERT: 0 178 THR cc_start: 0.7609 (t) cc_final: 0.6618 (p) REVERT: 0 222 LEU cc_start: 0.7816 (mp) cc_final: 0.7570 (mm) REVERT: 0 252 PRO cc_start: 0.8295 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: 2 145 VAL cc_start: 0.5694 (t) cc_final: 0.5393 (t) REVERT: 4 26 MET cc_start: 0.2504 (ptt) cc_final: 0.2125 (pmm) REVERT: 4 64 TYR cc_start: 0.6700 (p90) cc_final: 0.6344 (p90) REVERT: 4 201 MET cc_start: 0.2346 (pmm) cc_final: 0.1840 (ptm) outliers start: 0 outliers final: 0 residues processed: 889 average time/residue: 0.2783 time to fit residues: 375.0483 Evaluate side-chains 597 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 260 GLN A 325 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN F 83 GLN F 117 GLN ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN H 123 GLN H 166 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 260 GLN L 325 GLN N 117 GLN N 260 GLN N 325 GLN P 180 ASN P 325 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 ASN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 325 GLN ** Y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 ASN Y 260 GLN Y 325 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 325 GLN 0 117 GLN 0 299 GLN 0 303 ASN 0 325 GLN 2 303 ASN 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.085955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.071489 restraints weight = 275968.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.073017 restraints weight = 210268.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.074212 restraints weight = 166817.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.075209 restraints weight = 136565.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.076032 restraints weight = 114350.241| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 41757 Z= 0.297 Angle : 0.973 15.836 56592 Z= 0.533 Chirality : 0.064 0.640 6544 Planarity : 0.010 0.171 7120 Dihedral : 15.456 85.039 6528 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.92 % Allowed : 7.25 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.11), residues: 5216 helix: 0.63 (0.11), residues: 2288 sheet: 1.05 (0.18), residues: 816 loop : -1.17 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG D 225 TYR 0.031 0.003 TYR C 263 PHE 0.036 0.003 PHE U 216 TRP 0.006 0.001 TRP A 289 HIS 0.012 0.002 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00638 (41712) covalent geometry : angle 0.97281 (56592) hydrogen bonds : bond 0.05599 ( 1904) hydrogen bonds : angle 5.99576 ( 5472) Misc. bond : bond 0.00951 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 698 time to evaluate : 1.479 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 130 MET cc_start: 0.7824 (ttt) cc_final: 0.7590 (ttt) REVERT: A 158 MET cc_start: 0.8686 (mtp) cc_final: 0.7988 (ptp) REVERT: A 162 HIS cc_start: 0.7376 (m-70) cc_final: 0.7018 (m-70) REVERT: A 183 ASN cc_start: 0.9116 (m-40) cc_final: 0.8906 (m-40) REVERT: A 190 PHE cc_start: 0.8770 (m-10) cc_final: 0.8520 (m-10) REVERT: A 206 GLU cc_start: 0.8184 (mp0) cc_final: 0.7958 (mp0) REVERT: A 237 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 241 THR cc_start: 0.8504 (m) cc_final: 0.8238 (m) REVERT: A 268 TYR cc_start: 0.8630 (t80) cc_final: 0.8243 (t80) REVERT: A 317 VAL cc_start: 0.9213 (m) cc_final: 0.8782 (p) REVERT: C 57 LYS cc_start: 0.8533 (mtpt) cc_final: 0.7629 (mttp) REVERT: C 109 ASN cc_start: 0.7113 (t0) cc_final: 0.6836 (t0) REVERT: C 169 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8811 (pp) REVERT: C 201 MET cc_start: 0.6968 (pmm) cc_final: 0.6721 (pmm) REVERT: C 243 VAL cc_start: 0.7946 (t) cc_final: 0.7563 (m) REVERT: C 276 LEU cc_start: 0.8638 (mp) cc_final: 0.8378 (tp) REVERT: F 98 LEU cc_start: 0.5583 (pt) cc_final: 0.5253 (pt) REVERT: F 148 LEU cc_start: 0.8179 (mp) cc_final: 0.7945 (tt) REVERT: F 153 GLU cc_start: 0.3960 (mp0) cc_final: 0.3122 (mp0) REVERT: F 162 HIS cc_start: 0.7303 (m-70) cc_final: 0.6715 (m170) REVERT: F 170 MET cc_start: 0.7830 (mtm) cc_final: 0.7540 (mtt) REVERT: F 197 LYS cc_start: 0.6094 (mmtt) cc_final: 0.5520 (mmtt) REVERT: H 9 LEU cc_start: 0.9457 (tp) cc_final: 0.9130 (tt) REVERT: H 26 MET cc_start: 0.0585 (ptt) cc_final: 0.0254 (ptt) REVERT: H 169 LEU cc_start: 0.0680 (OUTLIER) cc_final: 0.0463 (mt) REVERT: J 74 LEU cc_start: 0.7363 (tp) cc_final: 0.7080 (mt) REVERT: J 169 LEU cc_start: 0.3485 (OUTLIER) cc_final: 0.2937 (tt) REVERT: J 290 TYR cc_start: 0.7735 (t80) cc_final: 0.7483 (t80) REVERT: L 31 HIS cc_start: 0.8529 (t70) cc_final: 0.8316 (t-170) REVERT: L 64 TYR cc_start: 0.6901 (p90) cc_final: 0.6689 (p90) REVERT: L 125 LEU cc_start: 0.8290 (mm) cc_final: 0.7766 (mt) REVERT: L 129 ASP cc_start: 0.7457 (m-30) cc_final: 0.7228 (m-30) REVERT: L 242 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7627 (ttp80) REVERT: L 244 LYS cc_start: 0.8188 (tttt) cc_final: 0.7736 (tptp) REVERT: L 254 PHE cc_start: 0.8527 (m-80) cc_final: 0.7945 (m-80) REVERT: L 256 GLN cc_start: 0.8153 (pp30) cc_final: 0.7356 (pp30) REVERT: L 290 TYR cc_start: 0.7686 (m-80) cc_final: 0.7318 (m-80) REVERT: N 27 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7209 (mtm180) REVERT: N 30 ASP cc_start: 0.8518 (t70) cc_final: 0.8270 (t0) REVERT: N 112 ASP cc_start: 0.9096 (t0) cc_final: 0.8791 (t0) REVERT: N 130 MET cc_start: 0.7118 (ttt) cc_final: 0.6818 (ttt) REVERT: N 155 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8489 (mm-30) REVERT: N 158 MET cc_start: 0.7566 (mtp) cc_final: 0.6729 (mmm) REVERT: N 196 MET cc_start: 0.7259 (ppp) cc_final: 0.6867 (ppp) REVERT: N 206 GLU cc_start: 0.8823 (mp0) cc_final: 0.8483 (mp0) REVERT: P 26 MET cc_start: -0.2106 (ptt) cc_final: -0.2511 (pmm) REVERT: P 151 LYS cc_start: 0.9134 (mttt) cc_final: 0.8933 (mttp) REVERT: P 185 ASN cc_start: 0.8781 (t0) cc_final: 0.8530 (t0) REVERT: P 222 LEU cc_start: 0.7351 (mp) cc_final: 0.6714 (mm) REVERT: P 276 LEU cc_start: 0.9233 (mp) cc_final: 0.8962 (tp) REVERT: P 303 ASN cc_start: 0.9357 (m-40) cc_final: 0.8949 (t0) REVERT: P 314 ILE cc_start: 0.7598 (mm) cc_final: 0.7310 (mm) REVERT: R 148 LEU cc_start: 0.8184 (mp) cc_final: 0.7909 (tt) REVERT: R 162 HIS cc_start: 0.7414 (m-70) cc_final: 0.7079 (m-70) REVERT: R 168 ARG cc_start: 0.6572 (ptp-170) cc_final: 0.6367 (ptm160) REVERT: R 169 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6924 (pp) REVERT: U 26 MET cc_start: 0.0174 (ptt) cc_final: -0.0842 (pmm) REVERT: U 64 TYR cc_start: 0.6273 (p90) cc_final: 0.5751 (p90) REVERT: U 141 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7466 (pt) REVERT: U 169 LEU cc_start: 0.1078 (OUTLIER) cc_final: -0.0211 (mt) REVERT: U 170 MET cc_start: 0.3704 (mmt) cc_final: 0.3272 (mmp) REVERT: U 268 TYR cc_start: 0.6079 (t80) cc_final: 0.5759 (t80) REVERT: U 301 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7365 (mmtt) REVERT: W 169 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.1804 (mp) REVERT: W 170 MET cc_start: 0.4338 (mmm) cc_final: 0.4097 (mmp) REVERT: Y 15 GLN cc_start: 0.9336 (tp-100) cc_final: 0.9069 (tp-100) REVERT: Y 16 ILE cc_start: 0.9162 (tp) cc_final: 0.8959 (tp) REVERT: Y 26 MET cc_start: 0.3279 (pmm) cc_final: 0.2446 (pmm) REVERT: Y 64 TYR cc_start: 0.6741 (p90) cc_final: 0.6513 (p90) REVERT: Y 242 ARG cc_start: 0.8742 (ttt-90) cc_final: 0.8106 (ttp80) REVERT: Y 244 LYS cc_start: 0.7799 (tttt) cc_final: 0.7435 (tptp) REVERT: Y 254 PHE cc_start: 0.8314 (m-80) cc_final: 0.7896 (m-80) REVERT: Y 256 GLN cc_start: 0.7908 (pp30) cc_final: 0.7276 (pp30) REVERT: D 26 MET cc_start: 0.1252 (pmm) cc_final: 0.0775 (pmm) REVERT: D 27 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7786 (mtm-85) REVERT: D 30 ASP cc_start: 0.8703 (t70) cc_final: 0.8035 (t0) REVERT: D 64 TYR cc_start: 0.8728 (p90) cc_final: 0.8118 (p90) REVERT: D 126 GLU cc_start: 0.8522 (pt0) cc_final: 0.7926 (pp20) REVERT: D 130 MET cc_start: 0.8962 (ttt) cc_final: 0.8682 (ttt) REVERT: D 151 LYS cc_start: 0.9460 (ptmm) cc_final: 0.8706 (tppt) REVERT: D 155 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 158 MET cc_start: 0.8248 (mtp) cc_final: 0.7573 (mtp) REVERT: D 180 ASN cc_start: 0.9495 (m-40) cc_final: 0.9087 (p0) REVERT: D 190 PHE cc_start: 0.9367 (m-80) cc_final: 0.9038 (m-10) REVERT: D 206 GLU cc_start: 0.8875 (mp0) cc_final: 0.8583 (mp0) REVERT: D 216 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: D 259 PHE cc_start: 0.8587 (p90) cc_final: 0.8384 (p90) REVERT: D 268 TYR cc_start: 0.8847 (t80) cc_final: 0.8279 (t80) REVERT: 0 81 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8986 (mm-30) REVERT: 0 148 LEU cc_start: 0.9245 (tt) cc_final: 0.9008 (tt) REVERT: 0 158 MET cc_start: 0.7711 (pmm) cc_final: 0.7360 (pmm) REVERT: 0 222 LEU cc_start: 0.8669 (mp) cc_final: 0.8262 (mm) REVERT: 0 268 TYR cc_start: 0.8537 (t80) cc_final: 0.8117 (t80) REVERT: 2 111 ASP cc_start: 0.6406 (m-30) cc_final: 0.5957 (m-30) REVERT: 2 133 ARG cc_start: 0.6411 (pmt-80) cc_final: 0.6137 (pmt-80) REVERT: 2 162 HIS cc_start: 0.6577 (m-70) cc_final: 0.6002 (m-70) REVERT: 2 192 ASN cc_start: 0.7608 (m110) cc_final: 0.7230 (m110) REVERT: 4 26 MET cc_start: 0.3711 (ptt) cc_final: 0.3050 (pmm) REVERT: 4 64 TYR cc_start: 0.7798 (p90) cc_final: 0.7308 (p90) REVERT: 4 170 MET cc_start: -0.1888 (ppp) cc_final: -0.2091 (ppp) REVERT: 4 201 MET cc_start: 0.2049 (pmm) cc_final: 0.1473 (ptm) outliers start: 38 outliers final: 10 residues processed: 725 average time/residue: 0.2576 time to fit residues: 288.2672 Evaluate side-chains 544 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 525 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 90 optimal weight: 0.7980 chunk 452 optimal weight: 20.0000 chunk 459 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 395 optimal weight: 4.9990 chunk 445 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 507 optimal weight: 7.9990 chunk 490 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN C 260 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 325 GLN J 325 GLN L 19 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 135 ASN P 325 GLN R 83 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 ASN R 325 GLN ** U 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN U 325 GLN W 325 GLN Y 325 GLN D 279 GLN D 325 GLN 0 303 ASN 0 325 GLN 2 303 ASN 2 325 GLN 4 15 GLN 4 325 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.084767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.069775 restraints weight = 266190.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.071360 restraints weight = 201747.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.072613 restraints weight = 159453.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.073628 restraints weight = 130304.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.074461 restraints weight = 109025.701| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 41757 Z= 0.213 Angle : 0.784 11.509 56592 Z= 0.421 Chirality : 0.055 0.450 6544 Planarity : 0.007 0.106 7120 Dihedral : 15.484 89.849 6528 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.29 % Allowed : 6.88 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.11), residues: 5216 helix: 0.44 (0.11), residues: 2288 sheet: 0.95 (0.18), residues: 816 loop : -1.21 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG U 221 TYR 0.174 0.008 TYR P 102 PHE 0.033 0.002 PHE Y 216 TRP 0.012 0.001 TRP A 289 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00438 (41712) covalent geometry : angle 0.78428 (56592) hydrogen bonds : bond 0.04627 ( 1904) hydrogen bonds : angle 5.65307 ( 5472) Misc. bond : bond 0.02268 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 640 time to evaluate : 1.519 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 130 MET cc_start: 0.7886 (ttt) cc_final: 0.7680 (ttt) REVERT: A 162 HIS cc_start: 0.7317 (m-70) cc_final: 0.6999 (m-70) REVERT: A 190 PHE cc_start: 0.8945 (m-10) cc_final: 0.8597 (m-10) REVERT: A 256 GLN cc_start: 0.9019 (pm20) cc_final: 0.8457 (pp30) REVERT: A 268 TYR cc_start: 0.8537 (t80) cc_final: 0.8163 (t80) REVERT: A 289 TRP cc_start: 0.9009 (m100) cc_final: 0.8683 (m100) REVERT: C 61 VAL cc_start: 0.6417 (t) cc_final: 0.6095 (m) REVERT: C 109 ASN cc_start: 0.7202 (t0) cc_final: 0.6988 (t0) REVERT: C 174 LEU cc_start: 0.9001 (mt) cc_final: 0.8682 (mt) REVERT: C 201 MET cc_start: 0.7169 (pmm) cc_final: 0.6916 (pmm) REVERT: C 276 LEU cc_start: 0.8721 (mp) cc_final: 0.8493 (tp) REVERT: F 98 LEU cc_start: 0.5743 (pt) cc_final: 0.5425 (pt) REVERT: F 153 GLU cc_start: 0.4189 (mp0) cc_final: 0.3518 (mp0) REVERT: F 162 HIS cc_start: 0.7475 (m-70) cc_final: 0.6888 (m170) REVERT: F 168 ARG cc_start: 0.6381 (ptp-170) cc_final: 0.6064 (ptm160) REVERT: F 189 ILE cc_start: 0.5545 (OUTLIER) cc_final: 0.4960 (mp) REVERT: H 9 LEU cc_start: 0.9445 (tp) cc_final: 0.9096 (tp) REVERT: H 196 MET cc_start: 0.4697 (mmp) cc_final: 0.4391 (mmp) REVERT: H 268 TYR cc_start: 0.5617 (t80) cc_final: 0.5362 (t80) REVERT: J 74 LEU cc_start: 0.7396 (tp) cc_final: 0.7069 (mt) REVERT: J 122 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7825 (tp30) REVERT: J 242 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7178 (ttp80) REVERT: J 244 LYS cc_start: 0.8034 (tttt) cc_final: 0.6416 (tmtt) REVERT: L 31 HIS cc_start: 0.8413 (t70) cc_final: 0.8178 (t-170) REVERT: L 125 LEU cc_start: 0.8342 (mm) cc_final: 0.7867 (mt) REVERT: L 129 ASP cc_start: 0.7455 (m-30) cc_final: 0.7247 (m-30) REVERT: L 158 MET cc_start: 0.5479 (mmp) cc_final: 0.4806 (mmp) REVERT: L 242 ARG cc_start: 0.8342 (ttt-90) cc_final: 0.7695 (ttp80) REVERT: L 244 LYS cc_start: 0.8191 (tttt) cc_final: 0.7691 (tptp) REVERT: L 254 PHE cc_start: 0.8561 (m-80) cc_final: 0.7740 (m-80) REVERT: L 256 GLN cc_start: 0.8207 (pp30) cc_final: 0.7463 (pp30) REVERT: L 290 TYR cc_start: 0.7673 (m-80) cc_final: 0.7405 (m-80) REVERT: N 18 ARG cc_start: 0.9113 (ptp-170) cc_final: 0.8889 (ptp-170) REVERT: N 112 ASP cc_start: 0.9130 (t0) cc_final: 0.8825 (t0) REVERT: N 130 MET cc_start: 0.7446 (ttt) cc_final: 0.7138 (ttt) REVERT: N 151 LYS cc_start: 0.9196 (ptmm) cc_final: 0.8981 (pttm) REVERT: N 206 GLU cc_start: 0.8797 (mp0) cc_final: 0.8429 (mp0) REVERT: N 256 GLN cc_start: 0.9096 (pp30) cc_final: 0.8802 (pp30) REVERT: N 320 LYS cc_start: 0.9352 (mtmm) cc_final: 0.9117 (ptpt) REVERT: P 26 MET cc_start: -0.2123 (ptt) cc_final: -0.2487 (pmm) REVERT: P 138 ASP cc_start: 0.7884 (t0) cc_final: 0.7637 (t0) REVERT: P 151 LYS cc_start: 0.9145 (mttt) cc_final: 0.8849 (mmtm) REVERT: P 162 HIS cc_start: 0.7047 (m170) cc_final: 0.6720 (m170) REVERT: P 185 ASN cc_start: 0.8846 (t0) cc_final: 0.8492 (t0) REVERT: P 222 LEU cc_start: 0.7582 (mp) cc_final: 0.6922 (mm) REVERT: P 245 VAL cc_start: 0.7606 (t) cc_final: 0.7336 (t) REVERT: P 276 LEU cc_start: 0.9217 (mp) cc_final: 0.8963 (tp) REVERT: P 303 ASN cc_start: 0.9354 (m-40) cc_final: 0.8999 (t0) REVERT: P 314 ILE cc_start: 0.7582 (mm) cc_final: 0.7381 (mm) REVERT: R 162 HIS cc_start: 0.7346 (m-70) cc_final: 0.7058 (m-70) REVERT: R 227 THR cc_start: 0.6985 (OUTLIER) cc_final: 0.6408 (p) REVERT: R 254 PHE cc_start: 0.6011 (m-10) cc_final: 0.5598 (m-10) REVERT: U 26 MET cc_start: -0.0247 (ptt) cc_final: -0.0978 (pmm) REVERT: U 170 MET cc_start: 0.5319 (mmt) cc_final: 0.3613 (tmm) REVERT: U 196 MET cc_start: 0.6597 (mmp) cc_final: 0.6325 (mmp) REVERT: U 268 TYR cc_start: 0.6216 (t80) cc_final: 0.5949 (t80) REVERT: W 196 MET cc_start: 0.7897 (mmp) cc_final: 0.7691 (mmp) REVERT: Y 15 GLN cc_start: 0.9365 (tp-100) cc_final: 0.9103 (tp-100) REVERT: Y 26 MET cc_start: 0.3238 (pmm) cc_final: 0.2345 (pmm) REVERT: Y 64 TYR cc_start: 0.6882 (p90) cc_final: 0.6575 (p90) REVERT: Y 158 MET cc_start: 0.7629 (mmp) cc_final: 0.6296 (mmp) REVERT: Y 162 HIS cc_start: 0.6601 (m-70) cc_final: 0.6328 (m170) REVERT: Y 197 LYS cc_start: 0.8662 (mptt) cc_final: 0.8434 (mmpt) REVERT: Y 242 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8075 (ttp80) REVERT: Y 244 LYS cc_start: 0.7849 (tttt) cc_final: 0.7489 (tptp) REVERT: Y 254 PHE cc_start: 0.8264 (m-80) cc_final: 0.7868 (m-80) REVERT: Y 256 GLN cc_start: 0.7932 (pp30) cc_final: 0.7287 (pp30) REVERT: D 27 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7905 (mtm-85) REVERT: D 30 ASP cc_start: 0.8728 (t70) cc_final: 0.8288 (t0) REVERT: D 64 TYR cc_start: 0.8608 (p90) cc_final: 0.8318 (p90) REVERT: D 130 MET cc_start: 0.8970 (ttt) cc_final: 0.8696 (ttt) REVERT: D 151 LYS cc_start: 0.9452 (ptmm) cc_final: 0.9008 (tppt) REVERT: D 180 ASN cc_start: 0.9447 (m-40) cc_final: 0.9032 (p0) REVERT: D 190 PHE cc_start: 0.9370 (m-80) cc_final: 0.9041 (m-10) REVERT: D 225 ARG cc_start: 0.7790 (mmt-90) cc_final: 0.7563 (mmt180) REVERT: D 244 LYS cc_start: 0.9219 (tppt) cc_final: 0.9012 (tppt) REVERT: D 268 TYR cc_start: 0.8523 (t80) cc_final: 0.7820 (t80) REVERT: 0 81 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8923 (mm-30) REVERT: 0 158 MET cc_start: 0.7691 (pmm) cc_final: 0.7241 (pmm) REVERT: 0 168 ARG cc_start: 0.9147 (ptp-170) cc_final: 0.8856 (ptp-110) REVERT: 0 222 LEU cc_start: 0.8698 (mp) cc_final: 0.8276 (mm) REVERT: 0 268 TYR cc_start: 0.8588 (t80) cc_final: 0.8176 (t80) REVERT: 2 111 ASP cc_start: 0.6279 (m-30) cc_final: 0.5845 (m-30) REVERT: 2 162 HIS cc_start: 0.6503 (m-70) cc_final: 0.5954 (m-70) REVERT: 4 26 MET cc_start: 0.3735 (ptt) cc_final: 0.2889 (pmm) REVERT: 4 64 TYR cc_start: 0.7771 (p90) cc_final: 0.7337 (p90) REVERT: 4 201 MET cc_start: 0.2194 (pmm) cc_final: 0.1641 (ptm) outliers start: 12 outliers final: 1 residues processed: 652 average time/residue: 0.2655 time to fit residues: 267.7001 Evaluate side-chains 514 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 511 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 311 optimal weight: 4.9990 chunk 447 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 188 optimal weight: 0.0370 chunk 97 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 453 optimal weight: 20.0000 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 135 ASN ** P 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN R 117 GLN R 162 HIS R 180 ASN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 325 GLN Y 325 GLN D 325 GLN 0 299 GLN 0 303 ASN 0 325 GLN 2 123 GLN 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.084286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.069398 restraints weight = 263716.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.070950 restraints weight = 200167.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.072194 restraints weight = 158792.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.073200 restraints weight = 129976.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.074009 restraints weight = 108809.816| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.590 41757 Z= 0.232 Angle : 0.811 65.307 56592 Z= 0.439 Chirality : 0.052 0.434 6544 Planarity : 0.007 0.272 7120 Dihedral : 15.275 89.875 6528 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.11), residues: 5216 helix: 0.55 (0.11), residues: 2288 sheet: 0.88 (0.18), residues: 832 loop : -1.26 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 221 TYR 0.588 0.008 TYR N 102 PHE 0.040 0.002 PHE H 216 TRP 0.014 0.001 TRP L 289 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00546 (41712) covalent geometry : angle 0.81088 (56592) hydrogen bonds : bond 0.04098 ( 1904) hydrogen bonds : angle 5.34020 ( 5472) Misc. bond : bond 0.01699 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 607 time to evaluate : 1.251 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8633 (p90) cc_final: 0.8308 (p90) REVERT: A 130 MET cc_start: 0.7891 (ttt) cc_final: 0.7690 (ttt) REVERT: A 162 HIS cc_start: 0.7247 (m-70) cc_final: 0.6831 (m170) REVERT: A 197 LYS cc_start: 0.8235 (tttp) cc_final: 0.7910 (tptt) REVERT: A 256 GLN cc_start: 0.9114 (pm20) cc_final: 0.8535 (pp30) REVERT: A 268 TYR cc_start: 0.8471 (t80) cc_final: 0.8161 (t80) REVERT: A 289 TRP cc_start: 0.8950 (m100) cc_final: 0.8625 (m100) REVERT: A 320 LYS cc_start: 0.9451 (ptpp) cc_final: 0.9179 (ptpp) REVERT: C 109 ASN cc_start: 0.7276 (t0) cc_final: 0.7049 (t0) REVERT: C 130 MET cc_start: 0.8124 (ttt) cc_final: 0.7885 (ttt) REVERT: C 162 HIS cc_start: 0.6898 (m170) cc_final: 0.6282 (m170) REVERT: C 174 LEU cc_start: 0.8918 (mt) cc_final: 0.8672 (mt) REVERT: C 201 MET cc_start: 0.7382 (pmm) cc_final: 0.7110 (pmm) REVERT: F 98 LEU cc_start: 0.5922 (pt) cc_final: 0.5460 (pt) REVERT: F 162 HIS cc_start: 0.7505 (m90) cc_final: 0.7186 (m170) REVERT: H 26 MET cc_start: -0.0160 (ptt) cc_final: -0.0473 (ptt) REVERT: H 268 TYR cc_start: 0.5519 (t80) cc_final: 0.4738 (t80) REVERT: H 301 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7767 (tptt) REVERT: J 74 LEU cc_start: 0.7424 (tp) cc_final: 0.7064 (mt) REVERT: J 122 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7536 (tp30) REVERT: J 244 LYS cc_start: 0.7534 (tttt) cc_final: 0.7199 (tptp) REVERT: L 31 HIS cc_start: 0.8335 (t70) cc_final: 0.8058 (t-170) REVERT: L 67 GLU cc_start: 0.7639 (tt0) cc_final: 0.7159 (tm-30) REVERT: L 125 LEU cc_start: 0.8427 (mm) cc_final: 0.7860 (mt) REVERT: L 126 GLU cc_start: 0.8711 (pt0) cc_final: 0.8386 (tp30) REVERT: L 143 ASP cc_start: 0.8569 (t0) cc_final: 0.8220 (t0) REVERT: L 158 MET cc_start: 0.5866 (mmp) cc_final: 0.4966 (mmp) REVERT: L 242 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7632 (ttp80) REVERT: L 244 LYS cc_start: 0.8199 (tttt) cc_final: 0.7789 (tptp) REVERT: L 254 PHE cc_start: 0.8422 (m-80) cc_final: 0.7728 (m-80) REVERT: L 256 GLN cc_start: 0.8201 (pp30) cc_final: 0.7567 (pp30) REVERT: N 112 ASP cc_start: 0.9041 (t0) cc_final: 0.8729 (t0) REVERT: N 130 MET cc_start: 0.7330 (ttt) cc_final: 0.7094 (ttt) REVERT: N 162 HIS cc_start: 0.7874 (m170) cc_final: 0.7567 (m170) REVERT: N 256 GLN cc_start: 0.9139 (pp30) cc_final: 0.8739 (pp30) REVERT: N 320 LYS cc_start: 0.9358 (mtmm) cc_final: 0.9120 (ptpp) REVERT: P 138 ASP cc_start: 0.7820 (t0) cc_final: 0.7551 (t0) REVERT: P 151 LYS cc_start: 0.9194 (mttt) cc_final: 0.8903 (mmtm) REVERT: P 162 HIS cc_start: 0.7246 (m170) cc_final: 0.6848 (m170) REVERT: P 222 LEU cc_start: 0.7587 (mp) cc_final: 0.6937 (mm) REVERT: P 245 VAL cc_start: 0.7734 (t) cc_final: 0.7300 (t) REVERT: P 276 LEU cc_start: 0.9238 (mp) cc_final: 0.8996 (tp) REVERT: P 303 ASN cc_start: 0.9353 (m-40) cc_final: 0.9066 (t0) REVERT: R 158 MET cc_start: 0.2878 (pmm) cc_final: 0.2648 (pmm) REVERT: U 26 MET cc_start: -0.0374 (ptt) cc_final: -0.0730 (pmm) REVERT: U 170 MET cc_start: 0.5563 (mmt) cc_final: 0.3778 (ttp) REVERT: U 196 MET cc_start: 0.6201 (mmp) cc_final: 0.5885 (mmm) REVERT: U 268 TYR cc_start: 0.5998 (t80) cc_final: 0.5711 (t80) REVERT: Y 26 MET cc_start: 0.2917 (pmm) cc_final: 0.1061 (ppp) REVERT: Y 64 TYR cc_start: 0.6741 (p90) cc_final: 0.6513 (p90) REVERT: Y 162 HIS cc_start: 0.6366 (m-70) cc_final: 0.5941 (m-70) REVERT: Y 197 LYS cc_start: 0.8914 (mptt) cc_final: 0.8621 (mmmt) REVERT: Y 242 ARG cc_start: 0.8883 (ttt-90) cc_final: 0.8384 (ttp80) REVERT: Y 244 LYS cc_start: 0.7978 (tttt) cc_final: 0.7577 (tptp) REVERT: Y 254 PHE cc_start: 0.8329 (m-80) cc_final: 0.7965 (m-80) REVERT: Y 256 GLN cc_start: 0.8160 (pp30) cc_final: 0.7604 (pp30) REVERT: D 26 MET cc_start: 0.0895 (pmm) cc_final: 0.0629 (pmm) REVERT: D 27 ARG cc_start: 0.8330 (mtt180) cc_final: 0.7838 (mtm-85) REVERT: D 30 ASP cc_start: 0.8658 (t70) cc_final: 0.8052 (t0) REVERT: D 130 MET cc_start: 0.8968 (ttt) cc_final: 0.8721 (ttt) REVERT: D 151 LYS cc_start: 0.9458 (ptmm) cc_final: 0.9024 (tppt) REVERT: D 162 HIS cc_start: 0.7180 (m170) cc_final: 0.6814 (m170) REVERT: D 180 ASN cc_start: 0.9418 (m-40) cc_final: 0.8994 (p0) REVERT: D 190 PHE cc_start: 0.9426 (m-80) cc_final: 0.9105 (m-10) REVERT: D 268 TYR cc_start: 0.8465 (t80) cc_final: 0.7673 (t80) REVERT: D 306 LYS cc_start: 0.9526 (pptt) cc_final: 0.9316 (ptmm) REVERT: D 320 LYS cc_start: 0.9609 (ptpp) cc_final: 0.9402 (pttm) REVERT: 0 81 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8889 (mm-30) REVERT: 0 158 MET cc_start: 0.7612 (pmm) cc_final: 0.7314 (pmm) REVERT: 0 168 ARG cc_start: 0.9164 (ptp-170) cc_final: 0.8886 (ptp-110) REVERT: 0 192 ASN cc_start: 0.6884 (t0) cc_final: 0.6396 (t0) REVERT: 0 201 MET cc_start: 0.6672 (pmm) cc_final: 0.6466 (pmm) REVERT: 0 222 LEU cc_start: 0.8688 (mp) cc_final: 0.8249 (mm) REVERT: 0 252 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8736 (Cg_endo) REVERT: 0 268 TYR cc_start: 0.8522 (t80) cc_final: 0.8254 (t80) REVERT: 2 64 TYR cc_start: 0.8507 (p90) cc_final: 0.8242 (p90) REVERT: 2 111 ASP cc_start: 0.6296 (m-30) cc_final: 0.5920 (m-30) REVERT: 2 162 HIS cc_start: 0.6832 (m-70) cc_final: 0.6284 (m-70) REVERT: 2 170 MET cc_start: 0.6039 (ppp) cc_final: 0.5748 (ppp) REVERT: 4 26 MET cc_start: 0.3962 (ptt) cc_final: 0.3026 (pmm) REVERT: 4 201 MET cc_start: 0.2089 (pmm) cc_final: 0.1559 (ptm) outliers start: 5 outliers final: 4 residues processed: 612 average time/residue: 0.2614 time to fit residues: 247.8370 Evaluate side-chains 491 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 487 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 472 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 389 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN C 260 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 325 GLN J 135 ASN J 325 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 ASN ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 85 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN ** P 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 ASN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 180 ASN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 96 HIS W 325 GLN Y 162 HIS Y 180 ASN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN 0 325 GLN 2 83 GLN 2 117 GLN 2 162 HIS 4 162 HIS ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.078830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.064333 restraints weight = 273253.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.065854 restraints weight = 207194.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067060 restraints weight = 164089.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.068014 restraints weight = 134388.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.068789 restraints weight = 113188.694| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 41757 Z= 0.268 Angle : 0.866 21.708 56592 Z= 0.461 Chirality : 0.054 0.421 6544 Planarity : 0.007 0.158 7120 Dihedral : 15.197 89.451 6528 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.11), residues: 5216 helix: 0.22 (0.10), residues: 2288 sheet: 0.61 (0.18), residues: 784 loop : -1.47 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 226 TYR 0.181 0.006 TYR N 102 PHE 0.037 0.003 PHE P 216 TRP 0.037 0.002 TRP N 289 HIS 0.015 0.002 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00571 (41712) covalent geometry : angle 0.86626 (56592) hydrogen bonds : bond 0.04638 ( 1904) hydrogen bonds : angle 5.56383 ( 5472) Misc. bond : bond 0.01183 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 640 time to evaluate : 1.403 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8864 (p90) cc_final: 0.8497 (p90) REVERT: A 162 HIS cc_start: 0.7327 (m-70) cc_final: 0.6956 (m170) REVERT: A 190 PHE cc_start: 0.8892 (m-10) cc_final: 0.8665 (m-10) REVERT: A 268 TYR cc_start: 0.8447 (t80) cc_final: 0.8165 (t80) REVERT: A 289 TRP cc_start: 0.9132 (m100) cc_final: 0.8444 (m100) REVERT: A 320 LYS cc_start: 0.9427 (ptpp) cc_final: 0.9210 (ptpp) REVERT: C 109 ASN cc_start: 0.7495 (t0) cc_final: 0.7268 (t0) REVERT: C 130 MET cc_start: 0.8273 (ttt) cc_final: 0.8061 (ttt) REVERT: C 222 LEU cc_start: 0.8243 (tp) cc_final: 0.7960 (tp) REVERT: F 98 LEU cc_start: 0.7025 (pt) cc_final: 0.6685 (pt) REVERT: F 162 HIS cc_start: 0.8032 (m90) cc_final: 0.7806 (m170) REVERT: H 26 MET cc_start: 0.1495 (ptt) cc_final: 0.1126 (ptt) REVERT: H 268 TYR cc_start: 0.6380 (t80) cc_final: 0.5543 (t80) REVERT: H 301 LYS cc_start: 0.8238 (mmtm) cc_final: 0.8007 (tppt) REVERT: J 26 MET cc_start: 0.1931 (pmm) cc_final: 0.1178 (pmm) REVERT: J 74 LEU cc_start: 0.7880 (tp) cc_final: 0.7446 (mt) REVERT: L 67 GLU cc_start: 0.8228 (tt0) cc_final: 0.8013 (tm-30) REVERT: L 119 ASP cc_start: 0.8456 (p0) cc_final: 0.8224 (p0) REVERT: L 125 LEU cc_start: 0.8558 (mm) cc_final: 0.8101 (mt) REVERT: L 126 GLU cc_start: 0.8826 (pt0) cc_final: 0.8529 (tp30) REVERT: L 129 ASP cc_start: 0.8006 (m-30) cc_final: 0.7598 (m-30) REVERT: L 133 ARG cc_start: 0.7516 (mmt180) cc_final: 0.7144 (ptp-110) REVERT: L 143 ASP cc_start: 0.8692 (t0) cc_final: 0.8333 (t0) REVERT: L 254 PHE cc_start: 0.8657 (m-80) cc_final: 0.8103 (m-80) REVERT: L 256 GLN cc_start: 0.8486 (pp30) cc_final: 0.8036 (pp30) REVERT: N 112 ASP cc_start: 0.9158 (t0) cc_final: 0.8860 (t0) REVERT: N 151 LYS cc_start: 0.9328 (ptpp) cc_final: 0.8822 (pttm) REVERT: N 162 HIS cc_start: 0.7769 (m170) cc_final: 0.7547 (m170) REVERT: N 256 GLN cc_start: 0.9124 (pp30) cc_final: 0.8719 (pp30) REVERT: N 320 LYS cc_start: 0.9401 (mtmm) cc_final: 0.9184 (ptpt) REVERT: P 28 MET cc_start: 0.5466 (mmp) cc_final: 0.5036 (mmp) REVERT: P 109 ASN cc_start: 0.8107 (t0) cc_final: 0.7888 (t0) REVERT: P 130 MET cc_start: 0.7943 (ttp) cc_final: 0.7308 (ttt) REVERT: P 162 HIS cc_start: 0.7425 (m170) cc_final: 0.6992 (m170) REVERT: P 201 MET cc_start: 0.7753 (pmm) cc_final: 0.7460 (pmm) REVERT: P 252 PRO cc_start: 0.8965 (Cg_exo) cc_final: 0.8698 (Cg_endo) REVERT: P 276 LEU cc_start: 0.9364 (mp) cc_final: 0.9144 (tp) REVERT: P 303 ASN cc_start: 0.9410 (m-40) cc_final: 0.9128 (t0) REVERT: R 158 MET cc_start: 0.4295 (pmm) cc_final: 0.3754 (pmm) REVERT: R 162 HIS cc_start: 0.8124 (m90) cc_final: 0.7848 (m-70) REVERT: U 13 LEU cc_start: 0.9261 (mt) cc_final: 0.8932 (pp) REVERT: U 26 MET cc_start: 0.1214 (ptt) cc_final: 0.0638 (pmm) REVERT: U 170 MET cc_start: 0.6031 (mmt) cc_final: 0.3744 (ttt) REVERT: U 196 MET cc_start: 0.6691 (mmp) cc_final: 0.6328 (mmm) REVERT: W 290 TYR cc_start: 0.7498 (t80) cc_final: 0.7260 (t80) REVERT: Y 26 MET cc_start: 0.3720 (pmm) cc_final: 0.1846 (ppp) REVERT: Y 64 TYR cc_start: 0.7156 (p90) cc_final: 0.6848 (p90) REVERT: Y 125 LEU cc_start: 0.9283 (mm) cc_final: 0.8883 (mt) REVERT: Y 129 ASP cc_start: 0.8173 (t70) cc_final: 0.7783 (m-30) REVERT: Y 153 GLU cc_start: 0.7627 (tt0) cc_final: 0.6557 (tp30) REVERT: Y 162 HIS cc_start: 0.6430 (m90) cc_final: 0.5319 (m-70) REVERT: Y 197 LYS cc_start: 0.9199 (mptt) cc_final: 0.8990 (mmmt) REVERT: Y 242 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8812 (mmm160) REVERT: Y 244 LYS cc_start: 0.8404 (tttt) cc_final: 0.8112 (tptp) REVERT: Y 254 PHE cc_start: 0.8476 (m-80) cc_final: 0.8127 (m-80) REVERT: Y 256 GLN cc_start: 0.8472 (pp30) cc_final: 0.7453 (pp30) REVERT: D 26 MET cc_start: 0.1970 (pmm) cc_final: 0.1625 (pmm) REVERT: D 27 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8199 (mtm-85) REVERT: D 30 ASP cc_start: 0.8823 (t70) cc_final: 0.8387 (t0) REVERT: D 67 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8709 (mm-30) REVERT: D 130 MET cc_start: 0.9226 (ttt) cc_final: 0.9005 (ttt) REVERT: D 151 LYS cc_start: 0.9498 (ptmm) cc_final: 0.9082 (tppt) REVERT: D 158 MET cc_start: 0.7785 (mtp) cc_final: 0.7357 (mtp) REVERT: D 162 HIS cc_start: 0.7211 (m170) cc_final: 0.6816 (m170) REVERT: D 180 ASN cc_start: 0.9444 (m-40) cc_final: 0.9009 (p0) REVERT: D 190 PHE cc_start: 0.9508 (m-80) cc_final: 0.9069 (m-10) REVERT: D 268 TYR cc_start: 0.8483 (t80) cc_final: 0.7746 (t80) REVERT: D 306 LYS cc_start: 0.9611 (pptt) cc_final: 0.9392 (ptmm) REVERT: 0 81 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9001 (mm-30) REVERT: 0 162 HIS cc_start: 0.6449 (m170) cc_final: 0.6094 (m170) REVERT: 0 168 ARG cc_start: 0.9159 (ptp-170) cc_final: 0.8860 (ptp-110) REVERT: 0 201 MET cc_start: 0.7071 (pmm) cc_final: 0.6839 (pmm) REVERT: 0 222 LEU cc_start: 0.8907 (mp) cc_final: 0.8299 (mm) REVERT: 2 162 HIS cc_start: 0.6919 (m90) cc_final: 0.6577 (m-70) REVERT: 2 170 MET cc_start: 0.6451 (ppp) cc_final: 0.6139 (ppp) REVERT: 4 201 MET cc_start: 0.1997 (pmm) cc_final: 0.1586 (ptm) outliers start: 3 outliers final: 0 residues processed: 642 average time/residue: 0.2615 time to fit residues: 261.1419 Evaluate side-chains 519 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 457 optimal weight: 8.9990 chunk 385 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 375 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 460 optimal weight: 7.9990 chunk 250 optimal weight: 0.0010 chunk 253 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 284 optimal weight: 0.9980 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN H 123 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN L 85 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 117 GLN N 299 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN P 325 GLN R 117 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 162 HIS W 325 GLN Y 325 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.078998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.064432 restraints weight = 265341.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.065962 restraints weight = 200347.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067190 restraints weight = 158661.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.068165 restraints weight = 129615.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.068902 restraints weight = 108804.957| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 41757 Z= 0.183 Angle : 0.739 12.347 56592 Z= 0.392 Chirality : 0.050 0.246 6544 Planarity : 0.006 0.101 7120 Dihedral : 14.968 89.364 6528 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.11), residues: 5216 helix: 0.38 (0.11), residues: 2272 sheet: 0.55 (0.18), residues: 800 loop : -1.27 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG 4 221 TYR 0.138 0.006 TYR N 102 PHE 0.027 0.002 PHE 2 216 TRP 0.033 0.001 TRP Y 289 HIS 0.005 0.001 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00395 (41712) covalent geometry : angle 0.73945 (56592) hydrogen bonds : bond 0.03958 ( 1904) hydrogen bonds : angle 5.33200 ( 5472) Misc. bond : bond 0.01367 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 1.504 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8854 (p90) cc_final: 0.8555 (p90) REVERT: A 130 MET cc_start: 0.8621 (ttt) cc_final: 0.8361 (ttt) REVERT: A 162 HIS cc_start: 0.7171 (m-70) cc_final: 0.6937 (m170) REVERT: A 256 GLN cc_start: 0.9142 (pm20) cc_final: 0.8586 (pp30) REVERT: A 268 TYR cc_start: 0.8454 (t80) cc_final: 0.8221 (t80) REVERT: A 289 TRP cc_start: 0.9046 (m100) cc_final: 0.8777 (m100) REVERT: A 320 LYS cc_start: 0.9457 (ptpp) cc_final: 0.9208 (ptpp) REVERT: C 109 ASN cc_start: 0.7618 (t0) cc_final: 0.7396 (t0) REVERT: C 162 HIS cc_start: 0.7294 (m170) cc_final: 0.6749 (m170) REVERT: F 98 LEU cc_start: 0.7121 (pt) cc_final: 0.6768 (pt) REVERT: F 162 HIS cc_start: 0.7957 (m90) cc_final: 0.7496 (m-70) REVERT: H 64 TYR cc_start: 0.6330 (p90) cc_final: 0.5776 (p90) REVERT: H 268 TYR cc_start: 0.6132 (t80) cc_final: 0.5143 (t80) REVERT: H 301 LYS cc_start: 0.8306 (mmtm) cc_final: 0.8009 (tppt) REVERT: J 74 LEU cc_start: 0.7892 (tp) cc_final: 0.7412 (mt) REVERT: J 259 PHE cc_start: 0.6564 (p90) cc_final: 0.6186 (p90) REVERT: L 26 MET cc_start: 0.4780 (pmm) cc_final: 0.2046 (ppp) REVERT: L 67 GLU cc_start: 0.8307 (tt0) cc_final: 0.7959 (tm-30) REVERT: L 119 ASP cc_start: 0.8445 (p0) cc_final: 0.8233 (p0) REVERT: L 125 LEU cc_start: 0.8637 (mm) cc_final: 0.8391 (mt) REVERT: L 143 ASP cc_start: 0.8631 (t0) cc_final: 0.8291 (t0) REVERT: L 158 MET cc_start: 0.7621 (mmp) cc_final: 0.6838 (mmm) REVERT: L 242 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.7902 (ttp80) REVERT: L 254 PHE cc_start: 0.8544 (m-80) cc_final: 0.8107 (m-80) REVERT: L 256 GLN cc_start: 0.8423 (pp30) cc_final: 0.8095 (pp30) REVERT: N 126 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7906 (pt0) REVERT: N 151 LYS cc_start: 0.9259 (ptpp) cc_final: 0.8886 (pttm) REVERT: N 256 GLN cc_start: 0.9151 (pp30) cc_final: 0.8719 (pp30) REVERT: N 320 LYS cc_start: 0.9416 (mtmm) cc_final: 0.9171 (ptpp) REVERT: P 28 MET cc_start: 0.4998 (mmp) cc_final: 0.4675 (mmp) REVERT: P 109 ASN cc_start: 0.8072 (t0) cc_final: 0.7871 (t0) REVERT: P 130 MET cc_start: 0.8016 (ttp) cc_final: 0.7448 (ttt) REVERT: P 162 HIS cc_start: 0.7476 (m170) cc_final: 0.7046 (m170) REVERT: P 222 LEU cc_start: 0.7990 (mp) cc_final: 0.7642 (mt) REVERT: P 252 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8760 (Cg_endo) REVERT: P 276 LEU cc_start: 0.9345 (mp) cc_final: 0.9109 (tp) REVERT: P 303 ASN cc_start: 0.9412 (m-40) cc_final: 0.9132 (t0) REVERT: R 158 MET cc_start: 0.3388 (pmm) cc_final: 0.2785 (pmm) REVERT: R 162 HIS cc_start: 0.8373 (m90) cc_final: 0.8110 (m-70) REVERT: U 13 LEU cc_start: 0.9304 (mt) cc_final: 0.8686 (pp) REVERT: U 26 MET cc_start: 0.0936 (ptt) cc_final: 0.0504 (pmm) REVERT: U 170 MET cc_start: 0.6345 (mmt) cc_final: 0.4026 (ttp) REVERT: U 196 MET cc_start: 0.7168 (mmp) cc_final: 0.6776 (mmm) REVERT: W 5 LYS cc_start: 0.8515 (tptt) cc_final: 0.7913 (pttm) REVERT: W 28 MET cc_start: 0.7301 (mmm) cc_final: 0.7070 (mmp) REVERT: W 290 TYR cc_start: 0.7487 (t80) cc_final: 0.7222 (t80) REVERT: Y 26 MET cc_start: 0.3711 (pmm) cc_final: 0.1621 (ppp) REVERT: Y 28 MET cc_start: 0.6744 (mmp) cc_final: 0.6317 (mmp) REVERT: Y 64 TYR cc_start: 0.7193 (p90) cc_final: 0.6873 (p90) REVERT: Y 125 LEU cc_start: 0.9308 (mm) cc_final: 0.8958 (mt) REVERT: Y 129 ASP cc_start: 0.8161 (t70) cc_final: 0.7846 (m-30) REVERT: Y 162 HIS cc_start: 0.6409 (m90) cc_final: 0.6085 (m-70) REVERT: Y 207 THR cc_start: 0.8699 (m) cc_final: 0.8479 (m) REVERT: Y 254 PHE cc_start: 0.8440 (m-80) cc_final: 0.8236 (m-80) REVERT: D 26 MET cc_start: 0.1649 (pmm) cc_final: 0.1243 (pmm) REVERT: D 27 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7960 (mtm-85) REVERT: D 30 ASP cc_start: 0.8730 (t70) cc_final: 0.8142 (t0) REVERT: D 64 TYR cc_start: 0.8727 (p90) cc_final: 0.8424 (p90) REVERT: D 67 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8614 (mt-10) REVERT: D 130 MET cc_start: 0.9236 (ttt) cc_final: 0.9005 (ttt) REVERT: D 151 LYS cc_start: 0.9471 (ptmm) cc_final: 0.9043 (tppt) REVERT: D 158 MET cc_start: 0.7197 (mtp) cc_final: 0.6885 (mtp) REVERT: D 162 HIS cc_start: 0.7161 (m170) cc_final: 0.6803 (m170) REVERT: D 180 ASN cc_start: 0.9385 (m-40) cc_final: 0.8915 (p0) REVERT: D 190 PHE cc_start: 0.9520 (m-80) cc_final: 0.9159 (m-10) REVERT: D 268 TYR cc_start: 0.8397 (t80) cc_final: 0.7818 (t80) REVERT: D 306 LYS cc_start: 0.9590 (pptt) cc_final: 0.9364 (ptmm) REVERT: 0 81 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8935 (mm-30) REVERT: 0 162 HIS cc_start: 0.6798 (m170) cc_final: 0.6416 (m170) REVERT: 0 168 ARG cc_start: 0.9144 (ptp-170) cc_final: 0.8887 (ptp-170) REVERT: 0 201 MET cc_start: 0.7259 (pmm) cc_final: 0.6992 (pmm) REVERT: 0 222 LEU cc_start: 0.8818 (mp) cc_final: 0.8144 (mm) REVERT: 0 268 TYR cc_start: 0.8457 (t80) cc_final: 0.8241 (t80) REVERT: 2 26 MET cc_start: 0.1976 (pmm) cc_final: 0.1722 (pmm) REVERT: 2 111 ASP cc_start: 0.6916 (m-30) cc_final: 0.6314 (m-30) REVERT: 2 162 HIS cc_start: 0.7401 (m90) cc_final: 0.7083 (m-70) REVERT: 2 166 GLN cc_start: 0.8274 (mp10) cc_final: 0.7797 (mp10) REVERT: 2 170 MET cc_start: 0.6647 (ppp) cc_final: 0.6314 (ppp) REVERT: 2 189 ILE cc_start: 0.6484 (tp) cc_final: 0.6258 (tp) REVERT: 4 26 MET cc_start: 0.5197 (ptt) cc_final: 0.3978 (pmm) REVERT: 4 201 MET cc_start: 0.1946 (pmm) cc_final: 0.1579 (ptm) outliers start: 2 outliers final: 1 residues processed: 605 average time/residue: 0.2634 time to fit residues: 246.7264 Evaluate side-chains 475 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 385 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 472 optimal weight: 7.9990 chunk 419 optimal weight: 0.3980 chunk 506 optimal weight: 20.0000 chunk 328 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 505 optimal weight: 0.3980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 HIS ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 117 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN P 183 ASN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 325 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 303 ASN ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN ** Y 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.077917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.063448 restraints weight = 266610.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.064941 restraints weight = 200742.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.066138 restraints weight = 158822.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.067108 restraints weight = 130017.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.067884 restraints weight = 109139.220| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 41757 Z= 0.178 Angle : 0.715 11.234 56592 Z= 0.380 Chirality : 0.049 0.215 6544 Planarity : 0.005 0.121 7120 Dihedral : 14.899 89.911 6528 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.11), residues: 5216 helix: 0.39 (0.11), residues: 2304 sheet: 0.62 (0.19), residues: 784 loop : -1.32 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 255 TYR 0.148 0.006 TYR D 102 PHE 0.023 0.002 PHE A 259 TRP 0.010 0.001 TRP 0 289 HIS 0.008 0.001 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00385 (41712) covalent geometry : angle 0.71457 (56592) hydrogen bonds : bond 0.03905 ( 1904) hydrogen bonds : angle 5.28623 ( 5472) Misc. bond : bond 0.01260 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.014 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8886 (p90) cc_final: 0.8509 (p90) REVERT: A 130 MET cc_start: 0.8691 (ttt) cc_final: 0.8392 (ttt) REVERT: A 183 ASN cc_start: 0.9074 (m110) cc_final: 0.8849 (m-40) REVERT: A 256 GLN cc_start: 0.9196 (pm20) cc_final: 0.8647 (pp30) REVERT: A 268 TYR cc_start: 0.8400 (t80) cc_final: 0.8177 (t80) REVERT: A 289 TRP cc_start: 0.9047 (m100) cc_final: 0.8427 (m100) REVERT: A 320 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9233 (ptpp) REVERT: C 109 ASN cc_start: 0.7807 (t0) cc_final: 0.7556 (t0) REVERT: F 98 LEU cc_start: 0.7472 (pt) cc_final: 0.7122 (pt) REVERT: F 148 LEU cc_start: 0.8274 (mm) cc_final: 0.8042 (mm) REVERT: H 244 LYS cc_start: 0.8416 (tmtt) cc_final: 0.7876 (tmtt) REVERT: H 268 TYR cc_start: 0.6295 (t80) cc_final: 0.5934 (t80) REVERT: J 26 MET cc_start: 0.2423 (pmm) cc_final: 0.1031 (ppp) REVERT: J 64 TYR cc_start: 0.7059 (p90) cc_final: 0.6843 (p90) REVERT: J 74 LEU cc_start: 0.8083 (tp) cc_final: 0.7793 (mt) REVERT: J 192 ASN cc_start: 0.2981 (t0) cc_final: 0.2655 (t0) REVERT: J 259 PHE cc_start: 0.6636 (p90) cc_final: 0.6243 (p90) REVERT: L 26 MET cc_start: 0.4814 (pmm) cc_final: 0.2061 (ppp) REVERT: L 143 ASP cc_start: 0.8651 (t0) cc_final: 0.8298 (t0) REVERT: L 158 MET cc_start: 0.7779 (mmp) cc_final: 0.6233 (mmm) REVERT: L 242 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.7887 (ttp80) REVERT: L 254 PHE cc_start: 0.8627 (m-80) cc_final: 0.8161 (m-80) REVERT: L 256 GLN cc_start: 0.8543 (pp30) cc_final: 0.8089 (pp30) REVERT: N 126 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8058 (mm-30) REVERT: N 130 MET cc_start: 0.7858 (ppp) cc_final: 0.7638 (ppp) REVERT: N 151 LYS cc_start: 0.9298 (ptpp) cc_final: 0.8913 (pttm) REVERT: N 162 HIS cc_start: 0.7840 (m170) cc_final: 0.7586 (m170) REVERT: N 165 LEU cc_start: 0.7942 (mm) cc_final: 0.7727 (mp) REVERT: N 256 GLN cc_start: 0.9109 (pp30) cc_final: 0.8677 (pp30) REVERT: N 320 LYS cc_start: 0.9390 (mtmm) cc_final: 0.9153 (ptpp) REVERT: P 28 MET cc_start: 0.5033 (mmp) cc_final: 0.4759 (mmp) REVERT: P 112 ASP cc_start: 0.8517 (m-30) cc_final: 0.8122 (t0) REVERT: P 151 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8907 (mmtm) REVERT: P 154 ILE cc_start: 0.8838 (mm) cc_final: 0.8523 (mt) REVERT: P 162 HIS cc_start: 0.7571 (m170) cc_final: 0.7143 (m170) REVERT: P 222 LEU cc_start: 0.8115 (mp) cc_final: 0.7832 (mt) REVERT: P 252 PRO cc_start: 0.9046 (Cg_exo) cc_final: 0.8811 (Cg_endo) REVERT: P 303 ASN cc_start: 0.9443 (m-40) cc_final: 0.9187 (t0) REVERT: R 148 LEU cc_start: 0.8508 (tt) cc_final: 0.8280 (mm) REVERT: R 158 MET cc_start: 0.3276 (pmm) cc_final: 0.2914 (pmm) REVERT: R 162 HIS cc_start: 0.8416 (m90) cc_final: 0.8168 (m-70) REVERT: R 254 PHE cc_start: 0.6804 (m-10) cc_final: 0.6379 (m-10) REVERT: U 13 LEU cc_start: 0.9263 (mt) cc_final: 0.8733 (pp) REVERT: U 26 MET cc_start: 0.0971 (ptt) cc_final: 0.0440 (pmm) REVERT: U 170 MET cc_start: 0.6472 (mmt) cc_final: 0.4109 (ttt) REVERT: U 196 MET cc_start: 0.7434 (mmp) cc_final: 0.6964 (mmm) REVERT: U 244 LYS cc_start: 0.7610 (mmpt) cc_final: 0.7391 (mmmt) REVERT: W 290 TYR cc_start: 0.7423 (t80) cc_final: 0.7117 (t80) REVERT: Y 26 MET cc_start: 0.3891 (pmm) cc_final: 0.2709 (pmm) REVERT: Y 64 TYR cc_start: 0.7259 (p90) cc_final: 0.6929 (p90) REVERT: Y 106 LEU cc_start: 0.9028 (tt) cc_final: 0.8744 (mm) REVERT: Y 125 LEU cc_start: 0.9321 (mm) cc_final: 0.8962 (mt) REVERT: Y 129 ASP cc_start: 0.8243 (t70) cc_final: 0.7898 (m-30) REVERT: Y 162 HIS cc_start: 0.6043 (m90) cc_final: 0.5781 (m170) REVERT: Y 207 THR cc_start: 0.8904 (m) cc_final: 0.8525 (m) REVERT: Y 244 LYS cc_start: 0.8518 (tttt) cc_final: 0.8276 (tptp) REVERT: D 26 MET cc_start: 0.1732 (pmm) cc_final: 0.1409 (pmm) REVERT: D 27 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7932 (mtm180) REVERT: D 30 ASP cc_start: 0.8651 (t70) cc_final: 0.7992 (t0) REVERT: D 151 LYS cc_start: 0.9468 (ptmm) cc_final: 0.9019 (tppt) REVERT: D 162 HIS cc_start: 0.7063 (m170) cc_final: 0.6832 (m170) REVERT: D 180 ASN cc_start: 0.9372 (m-40) cc_final: 0.8905 (p0) REVERT: D 190 PHE cc_start: 0.9508 (m-80) cc_final: 0.9156 (m-10) REVERT: D 268 TYR cc_start: 0.8392 (t80) cc_final: 0.7815 (t80) REVERT: 0 81 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8959 (mm-30) REVERT: 0 162 HIS cc_start: 0.7040 (m170) cc_final: 0.6659 (m170) REVERT: 0 168 ARG cc_start: 0.9155 (ptp-170) cc_final: 0.8914 (ptp-110) REVERT: 0 222 LEU cc_start: 0.8802 (mp) cc_final: 0.8115 (mm) REVERT: 2 162 HIS cc_start: 0.7569 (m90) cc_final: 0.7244 (m-70) REVERT: 2 170 MET cc_start: 0.6848 (ppp) cc_final: 0.6520 (ppp) REVERT: 4 201 MET cc_start: 0.1991 (pmm) cc_final: 0.1664 (ptm) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2586 time to fit residues: 246.7206 Evaluate side-chains 490 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 331 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 362 optimal weight: 1.9990 chunk 345 optimal weight: 0.0670 chunk 356 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 495 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 337 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 325 GLN J 325 GLN L 85 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 135 ASN P 212 ASN P 279 GLN P 325 GLN R 212 ASN R 325 GLN U 123 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 GLN W 325 GLN ** Y 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.079069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.064559 restraints weight = 261948.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.066084 restraints weight = 196735.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.067317 restraints weight = 155240.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.068257 restraints weight = 126553.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.069008 restraints weight = 106577.070| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.8062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 41757 Z= 0.156 Angle : 0.715 12.678 56592 Z= 0.375 Chirality : 0.048 0.218 6544 Planarity : 0.005 0.123 7120 Dihedral : 14.855 89.970 6528 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.02 % Allowed : 2.24 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.12), residues: 5216 helix: 0.59 (0.11), residues: 2272 sheet: 0.74 (0.19), residues: 784 loop : -1.19 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 4 221 TYR 0.152 0.005 TYR C 102 PHE 0.028 0.002 PHE U 190 TRP 0.011 0.001 TRP C 289 HIS 0.008 0.001 HIS H 162 Details of bonding type rmsd covalent geometry : bond 0.00337 (41712) covalent geometry : angle 0.71526 (56592) hydrogen bonds : bond 0.03819 ( 1904) hydrogen bonds : angle 5.24103 ( 5472) Misc. bond : bond 0.01251 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 593 time to evaluate : 1.426 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 26 MET cc_start: -0.0628 (ptt) cc_final: -0.0868 (ppp) REVERT: A 64 TYR cc_start: 0.8911 (p90) cc_final: 0.8530 (p90) REVERT: A 130 MET cc_start: 0.8744 (ttt) cc_final: 0.8407 (ttt) REVERT: A 183 ASN cc_start: 0.9039 (m110) cc_final: 0.8806 (m-40) REVERT: A 215 LYS cc_start: 0.9637 (ptpp) cc_final: 0.9229 (tmtt) REVERT: A 256 GLN cc_start: 0.9183 (pm20) cc_final: 0.8614 (pp30) REVERT: A 268 TYR cc_start: 0.8422 (t80) cc_final: 0.8199 (t80) REVERT: A 289 TRP cc_start: 0.8954 (m100) cc_final: 0.8318 (m100) REVERT: A 320 LYS cc_start: 0.9483 (ptpp) cc_final: 0.9250 (ptpp) REVERT: C 109 ASN cc_start: 0.7851 (t0) cc_final: 0.7592 (t0) REVERT: C 130 MET cc_start: 0.8040 (ppp) cc_final: 0.7696 (ppp) REVERT: F 26 MET cc_start: -0.0908 (ptp) cc_final: -0.1171 (ptp) REVERT: F 109 ASN cc_start: 0.7140 (t0) cc_final: 0.6836 (t0) REVERT: F 148 LEU cc_start: 0.8222 (mm) cc_final: 0.8015 (mm) REVERT: H 268 TYR cc_start: 0.6086 (t80) cc_final: 0.4758 (t80) REVERT: H 301 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8029 (tppt) REVERT: J 64 TYR cc_start: 0.7087 (p90) cc_final: 0.6843 (p90) REVERT: J 192 ASN cc_start: 0.2616 (t0) cc_final: 0.2113 (t0) REVERT: J 244 LYS cc_start: 0.8081 (mptt) cc_final: 0.7586 (tppt) REVERT: J 259 PHE cc_start: 0.6696 (p90) cc_final: 0.6493 (p90) REVERT: L 26 MET cc_start: 0.4596 (pmm) cc_final: 0.2360 (ppp) REVERT: L 143 ASP cc_start: 0.8707 (t0) cc_final: 0.8345 (t0) REVERT: L 157 GLU cc_start: 0.7549 (pp20) cc_final: 0.7226 (pp20) REVERT: L 158 MET cc_start: 0.6340 (mmp) cc_final: 0.4728 (mmm) REVERT: L 242 ARG cc_start: 0.8625 (ttt-90) cc_final: 0.7866 (ttp80) REVERT: L 254 PHE cc_start: 0.8618 (m-80) cc_final: 0.8157 (m-80) REVERT: L 256 GLN cc_start: 0.8554 (pp30) cc_final: 0.8057 (pp30) REVERT: L 323 ARG cc_start: 0.8818 (mmm160) cc_final: 0.8600 (tpp-160) REVERT: N 126 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7939 (mm-30) REVERT: N 151 LYS cc_start: 0.9178 (ptpp) cc_final: 0.8662 (pttm) REVERT: N 165 LEU cc_start: 0.7933 (mm) cc_final: 0.7655 (mp) REVERT: N 256 GLN cc_start: 0.9109 (pp30) cc_final: 0.8707 (pp30) REVERT: N 320 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9159 (ptpp) REVERT: P 112 ASP cc_start: 0.8508 (m-30) cc_final: 0.8076 (t0) REVERT: P 154 ILE cc_start: 0.8686 (mm) cc_final: 0.8468 (mt) REVERT: P 162 HIS cc_start: 0.7548 (m170) cc_final: 0.7139 (m170) REVERT: P 222 LEU cc_start: 0.7987 (mp) cc_final: 0.7683 (mt) REVERT: P 252 PRO cc_start: 0.9001 (Cg_exo) cc_final: 0.8751 (Cg_endo) REVERT: P 303 ASN cc_start: 0.9430 (m-40) cc_final: 0.9183 (t0) REVERT: R 61 VAL cc_start: 0.5326 (p) cc_final: 0.4974 (m) REVERT: R 162 HIS cc_start: 0.8478 (m90) cc_final: 0.8254 (m-70) REVERT: R 170 MET cc_start: 0.8334 (mpp) cc_final: 0.8049 (mpp) REVERT: R 254 PHE cc_start: 0.7055 (m-10) cc_final: 0.6459 (m-10) REVERT: R 255 ARG cc_start: 0.7812 (mmp80) cc_final: 0.7486 (mmm160) REVERT: U 13 LEU cc_start: 0.9260 (mt) cc_final: 0.9058 (pp) REVERT: W 5 LYS cc_start: 0.8575 (tptt) cc_final: 0.7965 (pttm) REVERT: W 290 TYR cc_start: 0.7488 (t80) cc_final: 0.7221 (t80) REVERT: Y 26 MET cc_start: 0.2941 (pmm) cc_final: 0.1410 (ppp) REVERT: Y 64 TYR cc_start: 0.7182 (p90) cc_final: 0.6896 (p90) REVERT: Y 106 LEU cc_start: 0.8993 (tt) cc_final: 0.8759 (mm) REVERT: Y 129 ASP cc_start: 0.8258 (t70) cc_final: 0.7923 (m-30) REVERT: Y 162 HIS cc_start: 0.5920 (m90) cc_final: 0.5713 (m-70) REVERT: Y 178 THR cc_start: 0.8429 (t) cc_final: 0.8071 (p) REVERT: D 27 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7815 (mtm-85) REVERT: D 30 ASP cc_start: 0.8650 (t70) cc_final: 0.7963 (t0) REVERT: D 91 PHE cc_start: 0.9114 (t80) cc_final: 0.8754 (t80) REVERT: D 155 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8949 (mm-30) REVERT: D 162 HIS cc_start: 0.6744 (m170) cc_final: 0.6504 (m170) REVERT: D 180 ASN cc_start: 0.9336 (m-40) cc_final: 0.8841 (p0) REVERT: D 190 PHE cc_start: 0.9494 (m-80) cc_final: 0.9178 (m-10) REVERT: D 268 TYR cc_start: 0.8384 (t80) cc_final: 0.7794 (t80) REVERT: 0 81 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8951 (mm-30) REVERT: 0 91 PHE cc_start: 0.8856 (t80) cc_final: 0.8645 (t80) REVERT: 0 151 LYS cc_start: 0.9009 (pttm) cc_final: 0.8761 (mmtm) REVERT: 0 158 MET cc_start: 0.7400 (pmm) cc_final: 0.7143 (pmm) REVERT: 0 162 HIS cc_start: 0.7147 (m170) cc_final: 0.6693 (m170) REVERT: 0 168 ARG cc_start: 0.9164 (ptp-170) cc_final: 0.8928 (ptp-170) REVERT: 0 208 THR cc_start: 0.7957 (t) cc_final: 0.7640 (m) REVERT: 0 222 LEU cc_start: 0.8731 (mp) cc_final: 0.8176 (mm) REVERT: 0 254 PHE cc_start: 0.9583 (m-10) cc_final: 0.9361 (m-80) REVERT: 0 268 TYR cc_start: 0.8736 (t80) cc_final: 0.8306 (t80) REVERT: 2 111 ASP cc_start: 0.7031 (m-30) cc_final: 0.6464 (m-30) REVERT: 2 162 HIS cc_start: 0.7620 (m90) cc_final: 0.7282 (m-70) REVERT: 2 170 MET cc_start: 0.7094 (ppp) cc_final: 0.6811 (ppp) REVERT: 2 189 ILE cc_start: 0.6414 (tp) cc_final: 0.6170 (tp) REVERT: 4 26 MET cc_start: 0.4995 (ptt) cc_final: 0.3807 (pmm) REVERT: 4 201 MET cc_start: 0.1998 (pmm) cc_final: 0.1695 (ptm) outliers start: 1 outliers final: 1 residues processed: 594 average time/residue: 0.2571 time to fit residues: 239.2923 Evaluate side-chains 473 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 361 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 354 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 418 optimal weight: 4.9990 chunk 425 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN H 123 GLN H 162 HIS ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN H 303 ASN H 325 GLN J 325 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 172 GLN ** N 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN P 279 GLN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN R 212 ASN R 325 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 85 GLN ** Y 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 117 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 180 ASN ** 2 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.076518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.062265 restraints weight = 270133.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.063733 restraints weight = 204304.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.064888 restraints weight = 161787.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.065795 restraints weight = 132703.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.066487 restraints weight = 112056.390| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.8731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 41757 Z= 0.195 Angle : 0.738 10.337 56592 Z= 0.390 Chirality : 0.048 0.261 6544 Planarity : 0.005 0.073 7120 Dihedral : 14.945 89.934 6528 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.02 % Allowed : 1.87 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.11), residues: 5216 helix: 0.46 (0.11), residues: 2272 sheet: 0.48 (0.19), residues: 800 loop : -1.23 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG U 7 TYR 0.158 0.006 TYR R 102 PHE 0.030 0.002 PHE U 190 TRP 0.008 0.001 TRP 0 289 HIS 0.011 0.001 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00426 (41712) covalent geometry : angle 0.73794 (56592) hydrogen bonds : bond 0.03936 ( 1904) hydrogen bonds : angle 5.30982 ( 5472) Misc. bond : bond 0.01105 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 616 time to evaluate : 1.354 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8895 (p90) cc_final: 0.8504 (p90) REVERT: A 130 MET cc_start: 0.8684 (ttt) cc_final: 0.8353 (ttt) REVERT: A 151 LYS cc_start: 0.9038 (tmmt) cc_final: 0.8488 (ttmt) REVERT: A 183 ASN cc_start: 0.8994 (m110) cc_final: 0.8765 (m-40) REVERT: A 215 LYS cc_start: 0.9619 (ptpp) cc_final: 0.9225 (tmtt) REVERT: A 256 GLN cc_start: 0.9212 (pm20) cc_final: 0.8635 (pp30) REVERT: A 268 TYR cc_start: 0.8371 (t80) cc_final: 0.8168 (t80) REVERT: A 289 TRP cc_start: 0.8969 (m100) cc_final: 0.8368 (m100) REVERT: A 320 LYS cc_start: 0.9483 (ptpp) cc_final: 0.9259 (ptpp) REVERT: C 109 ASN cc_start: 0.7728 (t0) cc_final: 0.7459 (t0) REVERT: C 130 MET cc_start: 0.7985 (ppp) cc_final: 0.7784 (ppp) REVERT: C 133 ARG cc_start: 0.9055 (mtm180) cc_final: 0.8754 (mtm180) REVERT: C 158 MET cc_start: 0.7743 (pmm) cc_final: 0.7501 (pmm) REVERT: F 98 LEU cc_start: 0.8067 (pt) cc_final: 0.6371 (pt) REVERT: F 109 ASN cc_start: 0.7222 (t0) cc_final: 0.6876 (t0) REVERT: F 148 LEU cc_start: 0.8270 (mm) cc_final: 0.8067 (mm) REVERT: F 151 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7535 (mmmt) REVERT: F 170 MET cc_start: 0.8583 (mpp) cc_final: 0.8375 (mpp) REVERT: F 254 PHE cc_start: 0.7553 (m-10) cc_final: 0.7257 (m-10) REVERT: J 15 GLN cc_start: 0.9254 (tt0) cc_final: 0.8866 (tm-30) REVERT: J 16 ILE cc_start: 0.8558 (tp) cc_final: 0.7696 (tp) REVERT: J 26 MET cc_start: 0.2019 (pmm) cc_final: 0.1107 (pmm) REVERT: J 64 TYR cc_start: 0.7130 (p90) cc_final: 0.6874 (p90) REVERT: J 192 ASN cc_start: 0.2610 (t0) cc_final: 0.2084 (t0) REVERT: J 259 PHE cc_start: 0.6755 (p90) cc_final: 0.6461 (p90) REVERT: L 26 MET cc_start: 0.4299 (pmm) cc_final: 0.1927 (ptt) REVERT: L 126 GLU cc_start: 0.8803 (pt0) cc_final: 0.8552 (tp30) REVERT: L 143 ASP cc_start: 0.8558 (t0) cc_final: 0.8228 (t0) REVERT: L 223 ASP cc_start: 0.7609 (t70) cc_final: 0.7378 (t0) REVERT: L 242 ARG cc_start: 0.8641 (ttt-90) cc_final: 0.7934 (ttp80) REVERT: L 254 PHE cc_start: 0.8733 (m-80) cc_final: 0.8334 (m-80) REVERT: L 256 GLN cc_start: 0.8582 (pp30) cc_final: 0.8129 (pp30) REVERT: N 18 ARG cc_start: 0.9182 (ptt-90) cc_final: 0.8885 (ptt180) REVERT: N 126 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8108 (pt0) REVERT: N 151 LYS cc_start: 0.9309 (ptpp) cc_final: 0.9002 (pttm) REVERT: N 165 LEU cc_start: 0.8062 (mm) cc_final: 0.7819 (mp) REVERT: N 256 GLN cc_start: 0.9066 (pp30) cc_final: 0.8652 (pp30) REVERT: P 28 MET cc_start: 0.5450 (mmp) cc_final: 0.4992 (mmp) REVERT: P 112 ASP cc_start: 0.8580 (m-30) cc_final: 0.8185 (t0) REVERT: P 154 ILE cc_start: 0.8833 (mm) cc_final: 0.8495 (mt) REVERT: P 170 MET cc_start: 0.8570 (ptp) cc_final: 0.8282 (ptt) REVERT: P 252 PRO cc_start: 0.9071 (Cg_exo) cc_final: 0.8808 (Cg_endo) REVERT: P 262 LEU cc_start: 0.8610 (tp) cc_final: 0.8402 (mt) REVERT: P 303 ASN cc_start: 0.9452 (m-40) cc_final: 0.9221 (t0) REVERT: R 109 ASN cc_start: 0.7389 (t0) cc_final: 0.7090 (t0) REVERT: R 255 ARG cc_start: 0.8168 (mmp80) cc_final: 0.7755 (mmm160) REVERT: U 13 LEU cc_start: 0.9240 (mt) cc_final: 0.8862 (pp) REVERT: U 26 MET cc_start: 0.1629 (pmm) cc_final: 0.0438 (pmm) REVERT: U 196 MET cc_start: 0.6782 (mmm) cc_final: 0.6511 (mmm) REVERT: U 223 ASP cc_start: 0.7110 (p0) cc_final: 0.6899 (p0) REVERT: U 244 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8231 (mmtm) REVERT: W 28 MET cc_start: 0.7423 (mmp) cc_final: 0.7127 (mmp) REVERT: W 112 ASP cc_start: 0.7551 (m-30) cc_final: 0.7055 (t0) REVERT: W 290 TYR cc_start: 0.7533 (t80) cc_final: 0.7195 (t80) REVERT: Y 26 MET cc_start: 0.3363 (pmm) cc_final: 0.2097 (pmm) REVERT: Y 64 TYR cc_start: 0.7357 (p90) cc_final: 0.7104 (p90) REVERT: Y 129 ASP cc_start: 0.8388 (t70) cc_final: 0.8024 (m-30) REVERT: Y 162 HIS cc_start: 0.6217 (m90) cc_final: 0.5958 (m170) REVERT: Y 178 THR cc_start: 0.8501 (t) cc_final: 0.8163 (p) REVERT: D 27 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7942 (mtm-85) REVERT: D 30 ASP cc_start: 0.8763 (t70) cc_final: 0.8372 (t0) REVERT: D 151 LYS cc_start: 0.9444 (ptmm) cc_final: 0.9002 (tppt) REVERT: D 180 ASN cc_start: 0.9343 (m-40) cc_final: 0.8857 (p0) REVERT: D 190 PHE cc_start: 0.9494 (m-80) cc_final: 0.9141 (m-10) REVERT: D 268 TYR cc_start: 0.8336 (t80) cc_final: 0.7865 (t80) REVERT: 0 91 PHE cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: 0 151 LYS cc_start: 0.9102 (pttm) cc_final: 0.8823 (mmtm) REVERT: 0 158 MET cc_start: 0.7614 (pmm) cc_final: 0.6056 (ptp) REVERT: 0 162 HIS cc_start: 0.7343 (m170) cc_final: 0.6841 (m170) REVERT: 0 168 ARG cc_start: 0.9135 (ptp-170) cc_final: 0.8887 (ptp-170) REVERT: 0 208 THR cc_start: 0.8285 (t) cc_final: 0.7988 (m) REVERT: 0 222 LEU cc_start: 0.8782 (mp) cc_final: 0.8089 (mm) REVERT: 0 268 TYR cc_start: 0.8592 (t80) cc_final: 0.8264 (t80) REVERT: 2 162 HIS cc_start: 0.7846 (m90) cc_final: 0.7513 (m-70) REVERT: 2 170 MET cc_start: 0.7227 (ppp) cc_final: 0.6941 (ppp) REVERT: 4 183 ASN cc_start: 0.3626 (t0) cc_final: 0.3423 (t0) REVERT: 4 201 MET cc_start: 0.2084 (pmm) cc_final: 0.1709 (ptm) outliers start: 1 outliers final: 0 residues processed: 617 average time/residue: 0.2526 time to fit residues: 243.6306 Evaluate side-chains 489 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 371 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 465 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 416 optimal weight: 0.0470 chunk 328 optimal weight: 3.9990 chunk 343 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 447 optimal weight: 0.9980 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN L 85 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 172 GLN N 325 GLN P 279 GLN P 325 GLN R 162 HIS R 212 ASN R 325 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 GLN W 325 GLN ** Y 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 260 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.078775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.063978 restraints weight = 257771.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.065452 restraints weight = 195105.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.066597 restraints weight = 155130.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067551 restraints weight = 128164.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.068286 restraints weight = 108652.282| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.8987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 41757 Z= 0.160 Angle : 0.725 9.641 56592 Z= 0.382 Chirality : 0.049 0.348 6544 Planarity : 0.005 0.096 7120 Dihedral : 14.833 89.931 6528 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.12), residues: 5216 helix: 0.55 (0.11), residues: 2240 sheet: 0.60 (0.19), residues: 784 loop : -1.12 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG 4 221 TYR 0.134 0.006 TYR H 102 PHE 0.030 0.002 PHE H 190 TRP 0.008 0.001 TRP A 289 HIS 0.004 0.001 HIS H 162 Details of bonding type rmsd covalent geometry : bond 0.00346 (41712) covalent geometry : angle 0.72488 (56592) hydrogen bonds : bond 0.03782 ( 1904) hydrogen bonds : angle 5.27145 ( 5472) Misc. bond : bond 0.01326 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10432 Ramachandran restraints generated. 5216 Oldfield, 0 Emsley, 5216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.541 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.8807 (p90) cc_final: 0.8413 (p90) REVERT: A 130 MET cc_start: 0.8792 (ttt) cc_final: 0.8427 (ttt) REVERT: A 183 ASN cc_start: 0.9010 (m110) cc_final: 0.8789 (m-40) REVERT: A 215 LYS cc_start: 0.9609 (ptpp) cc_final: 0.9248 (tmtt) REVERT: A 256 GLN cc_start: 0.9171 (pm20) cc_final: 0.8628 (pp30) REVERT: A 289 TRP cc_start: 0.8820 (m100) cc_final: 0.8269 (m100) REVERT: A 320 LYS cc_start: 0.9522 (ptpp) cc_final: 0.9316 (ptpp) REVERT: C 109 ASN cc_start: 0.7791 (t0) cc_final: 0.7589 (t0) REVERT: C 133 ARG cc_start: 0.9071 (mtm180) cc_final: 0.8792 (mtm180) REVERT: C 138 ASP cc_start: 0.7509 (t0) cc_final: 0.7239 (t0) REVERT: C 158 MET cc_start: 0.7708 (pmm) cc_final: 0.7442 (pmm) REVERT: C 259 PHE cc_start: 0.7836 (p90) cc_final: 0.7550 (p90) REVERT: F 6 LYS cc_start: 0.8887 (mmpt) cc_final: 0.8416 (mmtm) REVERT: F 98 LEU cc_start: 0.6955 (pt) cc_final: 0.6447 (pt) REVERT: F 109 ASN cc_start: 0.7217 (t0) cc_final: 0.6849 (t0) REVERT: F 254 PHE cc_start: 0.7214 (m-10) cc_final: 0.6936 (m-10) REVERT: H 109 ASN cc_start: 0.6271 (t0) cc_final: 0.5944 (t0) REVERT: J 15 GLN cc_start: 0.9343 (tt0) cc_final: 0.8939 (tm-30) REVERT: J 16 ILE cc_start: 0.8677 (tp) cc_final: 0.7829 (tp) REVERT: J 26 MET cc_start: 0.1945 (pmm) cc_final: 0.1220 (ppp) REVERT: J 64 TYR cc_start: 0.7124 (p90) cc_final: 0.6908 (p90) REVERT: J 122 GLU cc_start: 0.8720 (pm20) cc_final: 0.8420 (pm20) REVERT: J 259 PHE cc_start: 0.6936 (p90) cc_final: 0.6568 (p90) REVERT: L 26 MET cc_start: 0.4370 (pmm) cc_final: 0.2356 (ppp) REVERT: L 126 GLU cc_start: 0.8802 (pt0) cc_final: 0.8512 (tp30) REVERT: L 143 ASP cc_start: 0.8519 (t0) cc_final: 0.8204 (t0) REVERT: L 158 MET cc_start: 0.5048 (mmp) cc_final: 0.4470 (mmp) REVERT: L 242 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8024 (ttp80) REVERT: L 254 PHE cc_start: 0.8762 (m-80) cc_final: 0.8343 (m-80) REVERT: L 256 GLN cc_start: 0.8675 (pp30) cc_final: 0.8250 (pp30) REVERT: N 18 ARG cc_start: 0.9242 (ptt-90) cc_final: 0.8941 (ptt180) REVERT: N 126 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8112 (pt0) REVERT: N 130 MET cc_start: 0.8291 (ppp) cc_final: 0.8079 (ppp) REVERT: N 151 LYS cc_start: 0.9240 (ptpp) cc_final: 0.8678 (pttm) REVERT: N 165 LEU cc_start: 0.8060 (mm) cc_final: 0.7854 (mp) REVERT: N 256 GLN cc_start: 0.9053 (pp30) cc_final: 0.8657 (pp30) REVERT: N 307 TYR cc_start: 0.9617 (t80) cc_final: 0.9412 (t80) REVERT: N 320 LYS cc_start: 0.9557 (ptpt) cc_final: 0.9344 (ptpt) REVERT: P 28 MET cc_start: 0.5526 (mmp) cc_final: 0.5143 (mmp) REVERT: P 111 ASP cc_start: 0.7947 (m-30) cc_final: 0.7722 (m-30) REVERT: P 112 ASP cc_start: 0.8600 (m-30) cc_final: 0.8192 (t0) REVERT: P 154 ILE cc_start: 0.8779 (mm) cc_final: 0.8465 (mt) REVERT: P 252 PRO cc_start: 0.9030 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: P 303 ASN cc_start: 0.9456 (m-40) cc_final: 0.9218 (t0) REVERT: R 26 MET cc_start: -0.0436 (ptt) cc_final: -0.0947 (pmm) REVERT: R 109 ASN cc_start: 0.7358 (t0) cc_final: 0.7046 (t0) REVERT: R 130 MET cc_start: 0.8382 (mmp) cc_final: 0.8013 (mmp) REVERT: R 162 HIS cc_start: 0.8595 (m90) cc_final: 0.8274 (m170) REVERT: R 254 PHE cc_start: 0.7379 (m-10) cc_final: 0.6545 (m-10) REVERT: R 255 ARG cc_start: 0.8367 (mmp80) cc_final: 0.7893 (mmm160) REVERT: U 26 MET cc_start: 0.1524 (pmm) cc_final: 0.0200 (pmm) REVERT: U 196 MET cc_start: 0.6894 (mmm) cc_final: 0.6634 (mmm) REVERT: W 5 LYS cc_start: 0.8611 (tptt) cc_final: 0.8006 (pttm) REVERT: W 112 ASP cc_start: 0.7684 (m-30) cc_final: 0.7097 (t0) REVERT: W 290 TYR cc_start: 0.7697 (t80) cc_final: 0.7373 (t80) REVERT: Y 26 MET cc_start: 0.3406 (pmm) cc_final: 0.2161 (pmm) REVERT: Y 64 TYR cc_start: 0.7374 (p90) cc_final: 0.7052 (p90) REVERT: Y 106 LEU cc_start: 0.9019 (tt) cc_final: 0.8751 (mm) REVERT: Y 129 ASP cc_start: 0.8374 (t70) cc_final: 0.8044 (m-30) REVERT: Y 178 THR cc_start: 0.8508 (t) cc_final: 0.8111 (p) REVERT: Y 225 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7749 (mmm-85) REVERT: D 91 PHE cc_start: 0.9030 (t80) cc_final: 0.8768 (t80) REVERT: D 155 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8960 (mm-30) REVERT: D 158 MET cc_start: 0.7301 (ptp) cc_final: 0.6853 (ptp) REVERT: D 168 ARG cc_start: 0.9036 (ptp-170) cc_final: 0.8801 (ptp-110) REVERT: D 180 ASN cc_start: 0.9306 (m-40) cc_final: 0.8852 (p0) REVERT: D 190 PHE cc_start: 0.9478 (m-80) cc_final: 0.9173 (m-10) REVERT: D 259 PHE cc_start: 0.9010 (p90) cc_final: 0.8596 (p90) REVERT: D 268 TYR cc_start: 0.8493 (t80) cc_final: 0.7912 (t80) REVERT: D 289 TRP cc_start: 0.8379 (m100) cc_final: 0.7884 (m100) REVERT: 0 91 PHE cc_start: 0.9013 (t80) cc_final: 0.8644 (t80) REVERT: 0 130 MET cc_start: 0.8933 (ttp) cc_final: 0.8450 (ppp) REVERT: 0 158 MET cc_start: 0.7488 (pmm) cc_final: 0.7208 (pmm) REVERT: 0 162 HIS cc_start: 0.7379 (m170) cc_final: 0.6829 (m170) REVERT: 0 168 ARG cc_start: 0.9157 (ptp-170) cc_final: 0.8927 (ptp-170) REVERT: 0 208 THR cc_start: 0.8314 (t) cc_final: 0.8022 (m) REVERT: 0 222 LEU cc_start: 0.8631 (mp) cc_final: 0.8038 (mm) REVERT: 0 254 PHE cc_start: 0.9536 (m-80) cc_final: 0.9256 (m-80) REVERT: 0 268 TYR cc_start: 0.8490 (t80) cc_final: 0.8195 (t80) REVERT: 2 111 ASP cc_start: 0.7279 (m-30) cc_final: 0.6729 (m-30) REVERT: 2 162 HIS cc_start: 0.7846 (m90) cc_final: 0.7534 (m-70) REVERT: 2 170 MET cc_start: 0.7456 (ppp) cc_final: 0.7217 (ppp) REVERT: 2 189 ILE cc_start: 0.6404 (tp) cc_final: 0.6138 (tp) REVERT: 4 26 MET cc_start: 0.5218 (ptt) cc_final: 0.4093 (pmm) REVERT: 4 183 ASN cc_start: 0.3706 (t0) cc_final: 0.3497 (t0) REVERT: 4 201 MET cc_start: 0.1994 (pmm) cc_final: 0.1615 (ptm) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.2594 time to fit residues: 241.5062 Evaluate side-chains 483 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 338 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 396 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 131 optimal weight: 0.0170 chunk 263 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 HIS ** L 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 162 HIS N 172 GLN N 325 GLN P 279 GLN P 325 GLN R 212 ASN R 325 GLN U 162 HIS ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 GLN ** W 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 162 HIS ** Y 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.076712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.062290 restraints weight = 269184.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.063812 restraints weight = 202040.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.065019 restraints weight = 159185.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.065978 restraints weight = 129918.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.066747 restraints weight = 108895.758| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.9307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41757 Z= 0.156 Angle : 0.702 9.160 56592 Z= 0.368 Chirality : 0.048 0.398 6544 Planarity : 0.005 0.076 7120 Dihedral : 14.831 89.502 6528 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 5216 helix: 0.58 (0.11), residues: 2240 sheet: 0.54 (0.19), residues: 784 loop : -1.09 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG 4 221 TYR 0.110 0.006 TYR H 102 PHE 0.024 0.002 PHE Y 91 TRP 0.007 0.001 TRP 0 289 HIS 0.016 0.001 HIS J 162 Details of bonding type rmsd covalent geometry : bond 0.00336 (41712) covalent geometry : angle 0.70155 (56592) hydrogen bonds : bond 0.03703 ( 1904) hydrogen bonds : angle 5.21233 ( 5472) Misc. bond : bond 0.01276 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8163.63 seconds wall clock time: 141 minutes 24.54 seconds (8484.54 seconds total)