Starting phenix.real_space_refine on Tue Jul 7 01:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_19761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_19761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_19761.map" model { file = "/net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_19761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s70_19761/07_2026/8s70_19761.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.61, per 1000 atoms: 0.11 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: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.79 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: 10.17 Time building geometry restraints manager: 5.10 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=" O3B AGS R 402 " pdb=" PB AGS R 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3B AGS 2 402 " pdb=" PB AGS 2 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS J 402 " pdb=" PB AGS J 402 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS L 402 " pdb=" PB AGS L 402 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O3B AGS 0 402 " pdb=" PB AGS 0 402 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 41707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 55777 2.52 - 5.04: 606 5.04 - 7.57: 113 7.57 - 10.09: 80 10.09 - 12.61: 16 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 - 26.64: 24000 26.64 - 53.28: 960 53.28 - 79.91: 336 79.91 - 106.55: 64 106.55 - 133.19: 96 Dihedral angle restraints: 25456 sinusoidal: 10816 harmonic: 14640 Sorted by residual: dihedral pdb=" O1A AGS L 402 " pdb=" O3A AGS L 402 " pdb=" PA AGS L 402 " pdb=" PB AGS L 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.82 133.19 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.79 133.16 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual 82.37 -50.79 133.16 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 25453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4990 0.052 - 0.105: 1304 0.105 - 0.157: 202 0.157 - 0.209: 0 0.209 - 0.262: 16 Chirality restraints: 6512 Sorted by residual: chirality pdb=" C3' AGS L 402 " pdb=" C2' AGS L 402 " pdb=" C4' AGS L 402 " pdb=" O3' AGS L 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' AGS J 402 " pdb=" C2' AGS J 402 " pdb=" C4' AGS J 402 " pdb=" O3' AGS J 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' AGS Y 402 " pdb=" C2' AGS Y 402 " pdb=" C4' AGS Y 402 " pdb=" O3' AGS Y 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 6509 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: 0.17 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: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.870 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.200 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 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= 1.974 Angle : 0.792 12.610 56592 Z= 0.446 Chirality : 0.046 0.262 6512 Planarity : 0.004 0.044 7120 Dihedral : 18.425 133.188 16176 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 are 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/Z covalent geometry : bond 0.00520 / 0.29 (41712) covalent geometry : angle 0.79229 / 0.45 (56592) hydrogen bonds : bond 0.19642 / 13.01 ( 1904) hydrogen bonds : angle 7.40824 / 5.63 ( 5472) Misc. bond : bond 0.59462 / 38.49 ( 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 : 1.487 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: 0.6603 (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: -0.1559 (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: 0.6633 (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: 0.8576 (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: 0.6619 (p) REVERT: 0 222 LEU cc_start: 0.7816 (mp) cc_final: 0.7570 (mm) REVERT: 0 252 PRO cc_start: 0.8296 (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: 0.3064 time to fit residues: 414.1477 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 : 1.545 ------------------------------------------------------------------------------- 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... 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 260 GLN C 325 GLN F 83 GLN F 117 GLN ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 260 GLN L 325 GLN N 85 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 279 GLN 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 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 ASN ** Y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 260 GLN D 325 GLN 0 117 GLN 0 279 GLN 0 299 GLN 0 303 ASN 0 325 GLN 2 303 ASN 2 325 GLN 4 162 HIS 4 325 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.085534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.071098 restraints weight = 277113.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.072628 restraints weight = 210998.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.073830 restraints weight = 167042.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.074806 restraints weight = 136739.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.075626 restraints weight = 114278.804| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 41757 Z= 0.265 Angle : 0.996 14.753 56592 Z= 0.508 Chirality : 0.064 0.586 6512 Planarity : 0.009 0.168 7120 Dihedral : 22.500 172.461 6816 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.46 % Allowed : 7.03 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 5216 helix: 0.77 (0.11), residues: 2288 sheet: 1.11 (0.18), residues: 816 loop : -1.05 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 225 TYR 0.024 0.003 TYR 0 268 PHE 0.034 0.003 PHE J 216 TRP 0.007 0.001 TRP Y 289 HIS 0.011 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (41712) covalent geometry : angle 0.99599 / 0.51 (56592) hydrogen bonds : bond 0.05516 / 3.68 ( 1904) hydrogen bonds : angle 5.83336 / 4.40 ( 5472) Misc. bond : bond 0.00753 / 0.49 ( 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 722 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 703 time to evaluate : 1.389 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: 0.7836 (ttt) cc_final: 0.7587 (ttt) REVERT: A 162 HIS cc_start: 0.7359 (m-70) cc_final: 0.7061 (m-70) REVERT: A 183 ASN cc_start: 0.9107 (m-40) cc_final: 0.8899 (m-40) REVERT: A 190 PHE cc_start: 0.8678 (m-10) cc_final: 0.8443 (m-10) REVERT: A 206 GLU cc_start: 0.8125 (mp0) cc_final: 0.7881 (mp0) REVERT: A 237 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8084 (p) REVERT: A 241 THR cc_start: 0.8438 (m) cc_final: 0.8189 (m) REVERT: A 268 TYR cc_start: 0.8529 (t80) cc_final: 0.8193 (t80) REVERT: A 317 VAL cc_start: 0.9182 (m) cc_final: 0.8753 (p) REVERT: C 109 ASN cc_start: 0.7127 (t0) cc_final: 0.6849 (t0) REVERT: C 201 MET cc_start: 0.6990 (pmm) cc_final: 0.6749 (pmm) REVERT: C 243 VAL cc_start: 0.7962 (t) cc_final: 0.7575 (m) REVERT: C 276 LEU cc_start: 0.8612 (mp) cc_final: 0.8356 (tp) REVERT: F 98 LEU cc_start: 0.5572 (pt) cc_final: 0.5262 (pt) REVERT: F 153 GLU cc_start: 0.3618 (mp0) cc_final: 0.2833 (mp0) REVERT: F 162 HIS cc_start: 0.7291 (m-70) cc_final: 0.6888 (m-70) REVERT: F 197 LYS cc_start: 0.6308 (mmtt) cc_final: 0.5801 (mmtt) REVERT: H 9 LEU cc_start: 0.9410 (tp) cc_final: 0.9094 (tt) REVERT: H 26 MET cc_start: 0.0526 (ptt) cc_final: 0.0226 (ptt) REVERT: H 268 TYR cc_start: 0.5551 (t80) cc_final: 0.5088 (t80) REVERT: J 74 LEU cc_start: 0.7371 (tp) cc_final: 0.7086 (mt) REVERT: J 242 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7178 (ttp80) REVERT: J 244 LYS cc_start: 0.7874 (tttt) cc_final: 0.6258 (tmtt) REVERT: L 125 LEU cc_start: 0.8301 (mm) cc_final: 0.7747 (mt) REVERT: L 126 GLU cc_start: 0.8598 (pt0) cc_final: 0.8286 (tp30) REVERT: L 197 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7496 (mmmt) REVERT: L 221 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.6869 (ttp-110) REVERT: L 242 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7652 (ttp80) REVERT: L 244 LYS cc_start: 0.8218 (tttt) cc_final: 0.7787 (tptp) REVERT: L 254 PHE cc_start: 0.8439 (m-80) cc_final: 0.7865 (m-80) REVERT: L 256 GLN cc_start: 0.8162 (pp30) cc_final: 0.7398 (pp30) REVERT: L 290 TYR cc_start: 0.7603 (m-80) cc_final: 0.7242 (m-80) REVERT: N 26 MET cc_start: 0.0232 (ptt) cc_final: 0.0024 (pmm) REVERT: N 27 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7559 (mtt90) REVERT: N 112 ASP cc_start: 0.9052 (t0) cc_final: 0.8750 (t0) REVERT: N 130 MET cc_start: 0.7133 (ttt) cc_final: 0.6849 (ttt) REVERT: N 155 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8505 (mm-30) REVERT: N 158 MET cc_start: 0.7512 (mtp) cc_final: 0.6526 (mmm) REVERT: N 206 GLU cc_start: 0.8786 (mp0) cc_final: 0.8478 (mp0) REVERT: P 111 ASP cc_start: 0.7656 (m-30) cc_final: 0.7305 (m-30) REVERT: P 141 ILE cc_start: 0.7731 (mm) cc_final: 0.7516 (mp) REVERT: P 222 LEU cc_start: 0.7345 (mp) cc_final: 0.6723 (mm) REVERT: P 276 LEU cc_start: 0.9207 (mp) cc_final: 0.8937 (tp) REVERT: P 303 ASN cc_start: 0.9333 (m-40) cc_final: 0.8986 (t0) REVERT: P 314 ILE cc_start: 0.7605 (mm) cc_final: 0.7319 (mm) REVERT: R 26 MET cc_start: -0.1273 (ptt) cc_final: -0.1949 (pmm) REVERT: R 148 LEU cc_start: 0.8187 (mp) cc_final: 0.7938 (tt) REVERT: R 162 HIS cc_start: 0.7449 (m-70) cc_final: 0.7160 (m-70) REVERT: U 26 MET cc_start: 0.0031 (ptt) cc_final: -0.0905 (pmm) REVERT: U 64 TYR cc_start: 0.6147 (p90) cc_final: 0.5643 (p90) REVERT: U 169 LEU cc_start: 0.0742 (OUTLIER) cc_final: -0.0289 (mt) REVERT: U 170 MET cc_start: 0.3718 (mmt) cc_final: 0.3347 (mmp) REVERT: U 268 TYR cc_start: 0.6031 (t80) cc_final: 0.5729 (t80) REVERT: U 301 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7428 (mmtt) REVERT: Y 15 GLN cc_start: 0.9317 (tp-100) cc_final: 0.9062 (tp-100) REVERT: Y 16 ILE cc_start: 0.9144 (tp) cc_final: 0.8943 (tp) REVERT: Y 26 MET cc_start: 0.3283 (pmm) cc_final: 0.2449 (pmm) REVERT: Y 64 TYR cc_start: 0.6686 (p90) cc_final: 0.6485 (p90) REVERT: Y 153 GLU cc_start: 0.7355 (tt0) cc_final: 0.6673 (mm-30) REVERT: Y 162 HIS cc_start: 0.5243 (m-70) cc_final: 0.5010 (m-70) REVERT: Y 197 LYS cc_start: 0.8788 (mmpt) cc_final: 0.7871 (mmmt) REVERT: Y 242 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8101 (ttp80) REVERT: Y 244 LYS cc_start: 0.7837 (tttt) cc_final: 0.7457 (tptp) REVERT: Y 254 PHE cc_start: 0.8279 (m-80) cc_final: 0.7897 (m-80) REVERT: Y 256 GLN cc_start: 0.7945 (pp30) cc_final: 0.7238 (pp30) REVERT: D 26 MET cc_start: 0.1161 (pmm) cc_final: 0.0825 (pmm) REVERT: D 27 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7798 (mtm-85) REVERT: D 30 ASP cc_start: 0.8654 (t70) cc_final: 0.7979 (t0) REVERT: D 64 TYR cc_start: 0.8708 (p90) cc_final: 0.7961 (p90) REVERT: D 126 GLU cc_start: 0.8423 (pt0) cc_final: 0.7825 (pp20) REVERT: D 151 LYS cc_start: 0.9471 (ptmm) cc_final: 0.9025 (tppt) REVERT: D 158 MET cc_start: 0.8181 (mtp) cc_final: 0.7453 (mtp) REVERT: D 180 ASN cc_start: 0.9495 (m-40) cc_final: 0.9097 (p0) REVERT: D 190 PHE cc_start: 0.9365 (m-80) cc_final: 0.9003 (m-10) REVERT: D 206 GLU cc_start: 0.8868 (mp0) cc_final: 0.8615 (mp0) REVERT: D 216 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: D 268 TYR cc_start: 0.8824 (t80) cc_final: 0.8285 (t80) REVERT: 0 81 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8978 (mm-30) REVERT: 0 98 LEU cc_start: 0.8626 (pp) cc_final: 0.8134 (pp) REVERT: 0 148 LEU cc_start: 0.9264 (tt) cc_final: 0.9008 (tt) REVERT: 0 151 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8816 (mmtt) REVERT: 0 154 ILE cc_start: 0.8436 (mt) cc_final: 0.8141 (mt) REVERT: 0 158 MET cc_start: 0.7705 (pmm) cc_final: 0.7363 (pmm) REVERT: 0 222 LEU cc_start: 0.8673 (mp) cc_final: 0.8271 (mm) REVERT: 0 268 TYR cc_start: 0.8507 (t80) cc_final: 0.7989 (t80) REVERT: 0 289 TRP cc_start: 0.8542 (m100) cc_final: 0.8341 (m100) REVERT: 2 111 ASP cc_start: 0.6337 (m-30) cc_final: 0.5892 (m-30) REVERT: 2 130 MET cc_start: 0.8299 (mmp) cc_final: 0.8055 (mmp) REVERT: 2 133 ARG cc_start: 0.6409 (pmt-80) cc_final: 0.6136 (pmt-80) REVERT: 2 162 HIS cc_start: 0.6551 (m-70) cc_final: 0.5972 (m-70) REVERT: 4 26 MET cc_start: 0.3655 (ptt) cc_final: 0.3030 (pmm) REVERT: 4 64 TYR cc_start: 0.7772 (p90) cc_final: 0.7339 (p90) REVERT: 4 201 MET cc_start: 0.2136 (pmm) cc_final: 0.1566 (ptm) outliers start: 19 outliers final: 5 residues processed: 715 average time/residue: 0.2941 time to fit residues: 325.0564 Evaluate side-chains 542 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 534 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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: 10.0000 chunk 452 optimal weight: 20.0000 chunk 459 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 445 optimal weight: 0.4980 chunk 290 optimal weight: 9.9990 chunk 507 optimal weight: 6.9990 chunk 490 optimal weight: 0.0170 chunk 219 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 overall best weight: 4.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 325 GLN ** 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 19 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 325 GLN R 83 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 ASN R 279 GLN 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 96 HIS W 325 GLN ** Y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 279 GLN 0 303 ASN 0 325 GLN ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 303 ASN 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.081979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.067697 restraints weight = 281539.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.069173 restraints weight = 214419.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070353 restraints weight = 169966.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.071296 restraints weight = 138982.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072077 restraints weight = 116608.919| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 41757 Z= 0.228 Angle : 0.860 11.425 56592 Z= 0.437 Chirality : 0.055 0.424 6512 Planarity : 0.006 0.108 7120 Dihedral : 21.060 167.641 6816 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.78 % Allowed : 7.83 % Favored : 91.39 % 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 are not related in a simple way. whole: -0.16 (0.11), residues: 5216 helix: 0.55 (0.11), residues: 2288 sheet: 0.94 (0.18), residues: 800 loop : -1.20 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 242 TYR 0.112 0.004 TYR P 102 PHE 0.025 0.003 PHE J 216 TRP 0.015 0.001 TRP A 289 HIS 0.009 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (41712) covalent geometry : angle 0.86020 / 0.44 (56592) hydrogen bonds : bond 0.04461 / 2.97 ( 1904) hydrogen bonds : angle 5.49832 / 4.14 ( 5472) Misc. bond : bond 0.00919 / 0.63 ( 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 694 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 662 time to evaluate : 1.864 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: A 162 HIS cc_start: 0.7221 (m-70) cc_final: 0.6804 (m170) REVERT: A 190 PHE cc_start: 0.8917 (m-10) cc_final: 0.8631 (m-10) REVERT: A 259 PHE cc_start: 0.8829 (p90) cc_final: 0.8619 (p90) REVERT: A 268 TYR cc_start: 0.8449 (t80) cc_final: 0.8116 (t80) REVERT: A 289 TRP cc_start: 0.9022 (m100) cc_final: 0.8746 (m100) REVERT: A 320 LYS cc_start: 0.9516 (ptpp) cc_final: 0.9302 (ptpt) REVERT: C 109 ASN cc_start: 0.7373 (t0) cc_final: 0.7115 (t0) REVERT: C 162 HIS cc_start: 0.7051 (m170) cc_final: 0.6387 (m170) REVERT: C 243 VAL cc_start: 0.8130 (t) cc_final: 0.7641 (m) REVERT: C 276 LEU cc_start: 0.8752 (mp) cc_final: 0.8534 (tp) REVERT: F 148 LEU cc_start: 0.8378 (tt) cc_final: 0.8047 (mm) REVERT: F 153 GLU cc_start: 0.4439 (mp0) cc_final: 0.3989 (mp0) REVERT: F 162 HIS cc_start: 0.7797 (m-70) cc_final: 0.7169 (m170) REVERT: H 64 TYR cc_start: 0.6331 (p90) cc_final: 0.6069 (p90) REVERT: H 141 ILE cc_start: 0.7227 (mm) cc_final: 0.6872 (mm) REVERT: H 189 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6408 (mp) REVERT: H 205 PRO cc_start: 0.2810 (Cg_endo) cc_final: 0.2461 (Cg_exo) REVERT: H 244 LYS cc_start: 0.8448 (tmtt) cc_final: 0.7564 (tmtt) REVERT: H 268 TYR cc_start: 0.5653 (t80) cc_final: 0.5252 (t80) REVERT: J 74 LEU cc_start: 0.7618 (tp) cc_final: 0.7248 (mt) REVERT: J 236 VAL cc_start: 0.7434 (p) cc_final: 0.7169 (t) REVERT: J 320 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8825 (mttt) REVERT: L 31 HIS cc_start: 0.8296 (t-170) cc_final: 0.7971 (t-170) REVERT: L 125 LEU cc_start: 0.8547 (mm) cc_final: 0.8040 (mt) REVERT: L 126 GLU cc_start: 0.8824 (pt0) cc_final: 0.8437 (tp30) REVERT: L 242 ARG cc_start: 0.8461 (ttt-90) cc_final: 0.7759 (ttp80) REVERT: L 244 LYS cc_start: 0.8445 (tttt) cc_final: 0.7981 (tptp) REVERT: L 254 PHE cc_start: 0.8555 (m-80) cc_final: 0.7987 (m-80) REVERT: L 256 GLN cc_start: 0.8383 (pp30) cc_final: 0.7825 (pp30) REVERT: L 290 TYR cc_start: 0.7754 (m-80) cc_final: 0.7353 (m-80) REVERT: N 27 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7689 (mtt180) REVERT: N 112 ASP cc_start: 0.9133 (t0) cc_final: 0.8844 (t0) REVERT: N 130 MET cc_start: 0.7548 (ttt) cc_final: 0.7288 (ttt) REVERT: N 155 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8488 (mm-30) REVERT: N 206 GLU cc_start: 0.8758 (mp0) cc_final: 0.8265 (mp0) REVERT: N 256 GLN cc_start: 0.9078 (pp30) cc_final: 0.8702 (pp30) REVERT: N 320 LYS cc_start: 0.9554 (ptpt) cc_final: 0.9291 (ptpt) REVERT: P 109 ASN cc_start: 0.7888 (t0) cc_final: 0.7674 (t0) REVERT: P 111 ASP cc_start: 0.7935 (m-30) cc_final: 0.7523 (m-30) REVERT: P 130 MET cc_start: 0.7620 (ttt) cc_final: 0.6687 (ttt) REVERT: P 162 HIS cc_start: 0.7246 (m170) cc_final: 0.6857 (m170) REVERT: P 222 LEU cc_start: 0.7929 (mp) cc_final: 0.7223 (mm) REVERT: P 245 VAL cc_start: 0.8056 (t) cc_final: 0.7774 (t) REVERT: P 252 PRO cc_start: 0.8749 (Cg_exo) cc_final: 0.8508 (Cg_endo) REVERT: P 268 TYR cc_start: 0.8251 (t80) cc_final: 0.8048 (t80) REVERT: P 276 LEU cc_start: 0.9284 (mp) cc_final: 0.9022 (tp) REVERT: P 303 ASN cc_start: 0.9399 (m-40) cc_final: 0.9091 (t0) REVERT: R 26 MET cc_start: -0.0693 (ptt) cc_final: -0.2072 (pmm) REVERT: R 141 ILE cc_start: 0.6804 (mp) cc_final: 0.6584 (mp) REVERT: R 162 HIS cc_start: 0.7713 (m-70) cc_final: 0.7502 (m-70) REVERT: R 242 ARG cc_start: 0.8424 (ptt90) cc_final: 0.7984 (mtm110) REVERT: U 13 LEU cc_start: 0.9176 (mt) cc_final: 0.8806 (pp) REVERT: U 26 MET cc_start: 0.0663 (ptt) cc_final: -0.0370 (pmm) REVERT: U 196 MET cc_start: 0.6890 (mmp) cc_final: 0.6439 (mmm) REVERT: U 268 TYR cc_start: 0.6270 (t80) cc_final: 0.5913 (t80) REVERT: W 216 PHE cc_start: 0.1765 (OUTLIER) cc_final: 0.1374 (m-10) REVERT: W 290 TYR cc_start: 0.7788 (t80) cc_final: 0.7558 (t80) REVERT: Y 15 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9221 (tp-100) REVERT: Y 26 MET cc_start: 0.3337 (pmm) cc_final: 0.2649 (pmm) REVERT: Y 64 TYR cc_start: 0.6894 (p90) cc_final: 0.6611 (p90) REVERT: Y 242 ARG cc_start: 0.8881 (ttt-90) cc_final: 0.8143 (ttp80) REVERT: Y 244 LYS cc_start: 0.8196 (tttt) cc_final: 0.7755 (tptp) REVERT: Y 254 PHE cc_start: 0.8388 (m-80) cc_final: 0.8047 (m-80) REVERT: Y 256 GLN cc_start: 0.8077 (pp30) cc_final: 0.7248 (pp30) REVERT: D 27 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8001 (mtm-85) REVERT: D 30 ASP cc_start: 0.8777 (t70) cc_final: 0.8168 (t0) REVERT: D 105 LYS cc_start: 0.9405 (ptpt) cc_final: 0.9169 (pttm) REVERT: D 151 LYS cc_start: 0.9483 (ptmm) cc_final: 0.9035 (tppt) REVERT: D 162 HIS cc_start: 0.7209 (m170) cc_final: 0.6839 (m170) REVERT: D 180 ASN cc_start: 0.9428 (m-40) cc_final: 0.8993 (p0) REVERT: D 190 PHE cc_start: 0.9422 (m-80) cc_final: 0.9001 (m-10) REVERT: D 244 LYS cc_start: 0.9292 (tptp) cc_final: 0.8962 (tppt) REVERT: D 268 TYR cc_start: 0.8566 (t80) cc_final: 0.7754 (t80) REVERT: 0 81 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8955 (mm-30) REVERT: 0 158 MET cc_start: 0.7805 (pmm) cc_final: 0.7485 (pmm) REVERT: 0 168 ARG cc_start: 0.9152 (ptp-170) cc_final: 0.8831 (ptm160) REVERT: 0 189 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8064 (mp) REVERT: 0 222 LEU cc_start: 0.8939 (mp) cc_final: 0.8512 (mm) REVERT: 0 252 PRO cc_start: 0.9185 (Cg_exo) cc_final: 0.8958 (Cg_endo) REVERT: 0 268 TYR cc_start: 0.8607 (t80) cc_final: 0.8260 (t80) REVERT: 2 28 MET cc_start: 0.4522 (mmp) cc_final: 0.4310 (mmp) REVERT: 2 64 TYR cc_start: 0.8563 (p90) cc_final: 0.8358 (p90) REVERT: 2 111 ASP cc_start: 0.6703 (m-30) cc_final: 0.6302 (m-30) REVERT: 2 148 LEU cc_start: 0.8856 (mp) cc_final: 0.8650 (mp) REVERT: 2 162 HIS cc_start: 0.6989 (m-70) cc_final: 0.6374 (m-70) REVERT: 2 170 MET cc_start: 0.6215 (ppp) cc_final: 0.5953 (ppp) REVERT: 2 192 ASN cc_start: 0.7835 (m110) cc_final: 0.7491 (m110) REVERT: 4 26 MET cc_start: 0.4960 (ptt) cc_final: 0.4450 (ptp) REVERT: 4 64 TYR cc_start: 0.7790 (p90) cc_final: 0.7367 (p90) REVERT: 4 189 ILE cc_start: 0.8620 (pt) cc_final: 0.8389 (mp) REVERT: 4 201 MET cc_start: 0.1891 (pmm) cc_final: 0.1348 (ptm) outliers start: 32 outliers final: 2 residues processed: 692 average time/residue: 0.3014 time to fit residues: 321.9536 Evaluate side-chains 525 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 520 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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: 0.5980 chunk 447 optimal weight: 0.0020 chunk 355 optimal weight: 7.9990 chunk 188 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 453 optimal weight: 8.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 325 GLN C 325 GLN F 162 HIS ** 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 192 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN P 325 GLN R 117 GLN R 162 HIS R 180 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 325 GLN W 325 GLN Y 162 HIS Y 192 ASN Y 260 GLN Y 325 GLN D 325 GLN 0 15 GLN 0 279 GLN 0 299 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 GLN 2 162 HIS 2 325 GLN 4 325 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.083162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.068293 restraints weight = 263719.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.069836 restraints weight = 199371.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.071056 restraints weight = 157539.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072013 restraints weight = 128863.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.072841 restraints weight = 108345.382| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 41757 Z= 0.178 Angle : 0.810 9.710 56592 Z= 0.400 Chirality : 0.052 0.428 6512 Planarity : 0.006 0.067 7120 Dihedral : 20.656 166.837 6816 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % 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 are not related in a simple way. whole: -0.09 (0.11), residues: 5216 helix: 0.65 (0.11), residues: 2288 sheet: 0.89 (0.18), residues: 800 loop : -1.20 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 221 TYR 0.118 0.006 TYR N 102 PHE 0.053 0.002 PHE 0 216 TRP 0.012 0.001 TRP 0 289 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (41712) covalent geometry : angle 0.81035 / 0.40 (56592) hydrogen bonds : bond 0.03988 / 2.69 ( 1904) hydrogen bonds : angle 5.24124 / 3.91 ( 5472) Misc. bond : bond 0.01228 / 0.78 ( 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 624 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 614 time to evaluate : 1.886 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: A 64 TYR cc_start: 0.8844 (p90) cc_final: 0.8581 (p90) REVERT: A 130 MET cc_start: 0.8163 (ttt) cc_final: 0.7882 (ttt) REVERT: A 162 HIS cc_start: 0.7123 (m-70) cc_final: 0.6746 (m170) REVERT: A 217 TYR cc_start: 0.8857 (m-80) cc_final: 0.8642 (m-10) REVERT: A 268 TYR cc_start: 0.8622 (t80) cc_final: 0.8221 (t80) REVERT: A 320 LYS cc_start: 0.9490 (ptpp) cc_final: 0.9238 (ptpp) REVERT: C 109 ASN cc_start: 0.7345 (t0) cc_final: 0.7131 (t0) REVERT: C 151 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8576 (mmmt) REVERT: C 162 HIS cc_start: 0.7118 (m170) cc_final: 0.6537 (m170) REVERT: C 174 LEU cc_start: 0.9056 (mt) cc_final: 0.8678 (mt) REVERT: C 196 MET cc_start: 0.6897 (ppp) cc_final: 0.6629 (ppp) REVERT: C 243 VAL cc_start: 0.8186 (t) cc_final: 0.7627 (m) REVERT: C 276 LEU cc_start: 0.8805 (mp) cc_final: 0.8605 (tp) REVERT: F 162 HIS cc_start: 0.7602 (m90) cc_final: 0.7085 (m170) REVERT: F 189 ILE cc_start: 0.5479 (tt) cc_final: 0.4934 (mp) REVERT: F 254 PHE cc_start: 0.5766 (m-10) cc_final: 0.5555 (m-10) REVERT: H 26 MET cc_start: 0.0140 (ptt) cc_final: -0.0157 (ptt) REVERT: H 268 TYR cc_start: 0.5770 (t80) cc_final: 0.5380 (t80) REVERT: H 291 SER cc_start: 0.4226 (m) cc_final: 0.4022 (m) REVERT: J 26 MET cc_start: 0.1769 (pmm) cc_final: 0.1427 (pmm) REVERT: J 122 GLU cc_start: 0.8623 (pp20) cc_final: 0.7573 (tt0) REVERT: J 197 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7867 (mmtt) REVERT: J 320 LYS cc_start: 0.9278 (mtmm) cc_final: 0.8831 (mttt) REVERT: L 31 HIS cc_start: 0.8254 (t-170) cc_final: 0.7985 (t-170) REVERT: L 125 LEU cc_start: 0.8559 (mm) cc_final: 0.8044 (mt) REVERT: L 126 GLU cc_start: 0.8797 (pt0) cc_final: 0.8429 (tp30) REVERT: L 129 ASP cc_start: 0.8050 (m-30) cc_final: 0.7219 (m-30) REVERT: L 143 ASP cc_start: 0.8699 (t0) cc_final: 0.8319 (t0) REVERT: L 158 MET cc_start: 0.6108 (mmp) cc_final: 0.5653 (mmp) REVERT: L 221 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7490 (ttp-110) REVERT: L 242 ARG cc_start: 0.8569 (ttt-90) cc_final: 0.7786 (ttp80) REVERT: L 244 LYS cc_start: 0.8404 (tttt) cc_final: 0.8005 (tptp) REVERT: L 254 PHE cc_start: 0.8565 (m-80) cc_final: 0.7959 (m-80) REVERT: L 256 GLN cc_start: 0.8286 (pp30) cc_final: 0.7599 (pp30) REVERT: L 290 TYR cc_start: 0.7705 (m-80) cc_final: 0.7296 (m-80) REVERT: N 18 ARG cc_start: 0.9229 (ptp-170) cc_final: 0.8968 (ptt-90) REVERT: N 27 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7415 (mtt90) REVERT: N 112 ASP cc_start: 0.9177 (t0) cc_final: 0.8829 (t0) REVERT: N 130 MET cc_start: 0.7448 (ttt) cc_final: 0.7230 (ttt) REVERT: N 155 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8486 (mm-30) REVERT: N 162 HIS cc_start: 0.7939 (m170) cc_final: 0.7674 (m170) REVERT: N 256 GLN cc_start: 0.9073 (pp30) cc_final: 0.8733 (pp30) REVERT: N 320 LYS cc_start: 0.9520 (ptpt) cc_final: 0.9224 (ptpp) REVERT: P 28 MET cc_start: 0.5123 (mmp) cc_final: 0.4812 (mmp) REVERT: P 109 ASN cc_start: 0.7946 (t0) cc_final: 0.7722 (t0) REVERT: P 145 VAL cc_start: 0.8347 (t) cc_final: 0.7752 (t) REVERT: P 148 LEU cc_start: 0.9057 (tt) cc_final: 0.8734 (mp) REVERT: P 162 HIS cc_start: 0.7468 (m170) cc_final: 0.7072 (m170) REVERT: P 201 MET cc_start: 0.7842 (pmm) cc_final: 0.7623 (pmm) REVERT: P 222 LEU cc_start: 0.7793 (mp) cc_final: 0.7297 (mt) REVERT: P 252 PRO cc_start: 0.8714 (Cg_exo) cc_final: 0.8409 (Cg_endo) REVERT: P 268 TYR cc_start: 0.8421 (t80) cc_final: 0.8148 (t80) REVERT: P 276 LEU cc_start: 0.9271 (mp) cc_final: 0.9041 (tp) REVERT: P 303 ASN cc_start: 0.9405 (m-40) cc_final: 0.9094 (t0) REVERT: R 158 MET cc_start: 0.4043 (pmm) cc_final: 0.3800 (pmm) REVERT: R 196 MET cc_start: 0.5111 (tpt) cc_final: 0.4867 (tpt) REVERT: R 242 ARG cc_start: 0.8424 (ptt90) cc_final: 0.8025 (mtm110) REVERT: U 13 LEU cc_start: 0.9210 (mt) cc_final: 0.8880 (pp) REVERT: U 26 MET cc_start: 0.0002 (ptt) cc_final: -0.0767 (pmm) REVERT: U 268 TYR cc_start: 0.6092 (t80) cc_final: 0.5736 (t80) REVERT: W 290 TYR cc_start: 0.7600 (t80) cc_final: 0.7390 (t80) REVERT: Y 26 MET cc_start: 0.3316 (pmm) cc_final: 0.1308 (ppp) REVERT: Y 64 TYR cc_start: 0.6738 (p90) cc_final: 0.6509 (p90) REVERT: Y 197 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8954 (mmmt) REVERT: Y 207 THR cc_start: 0.8497 (m) cc_final: 0.8241 (p) REVERT: Y 242 ARG cc_start: 0.8872 (ttt-90) cc_final: 0.8113 (ttp80) REVERT: Y 244 LYS cc_start: 0.8097 (tttt) cc_final: 0.7696 (tptp) REVERT: Y 254 PHE cc_start: 0.8354 (m-80) cc_final: 0.8029 (m-80) REVERT: Y 256 GLN cc_start: 0.8010 (pp30) cc_final: 0.7271 (pp30) REVERT: D 27 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7935 (mtm-85) REVERT: D 30 ASP cc_start: 0.8746 (t70) cc_final: 0.8310 (t0) REVERT: D 105 LYS cc_start: 0.9436 (ptpt) cc_final: 0.9195 (pttm) REVERT: D 126 GLU cc_start: 0.8618 (pt0) cc_final: 0.8131 (pp20) REVERT: D 151 LYS cc_start: 0.9460 (ptmm) cc_final: 0.9038 (tppt) REVERT: D 162 HIS cc_start: 0.7133 (m170) cc_final: 0.6763 (m170) REVERT: D 180 ASN cc_start: 0.9334 (m-40) cc_final: 0.8888 (p0) REVERT: D 190 PHE cc_start: 0.9448 (m-80) cc_final: 0.9081 (m-10) REVERT: D 268 TYR cc_start: 0.8546 (t80) cc_final: 0.7695 (t80) REVERT: D 306 LYS cc_start: 0.9557 (pptt) cc_final: 0.9352 (ptmm) REVERT: 0 28 MET cc_start: 0.6139 (mmm) cc_final: 0.5901 (mmp) REVERT: 0 81 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8880 (mm-30) REVERT: 0 158 MET cc_start: 0.7579 (pmm) cc_final: 0.7181 (pmm) REVERT: 0 162 HIS cc_start: 0.6133 (m170) cc_final: 0.5850 (m170) REVERT: 0 222 LEU cc_start: 0.8784 (mp) cc_final: 0.8244 (mm) REVERT: 0 252 PRO cc_start: 0.9207 (Cg_exo) cc_final: 0.8978 (Cg_endo) REVERT: 0 268 TYR cc_start: 0.8604 (t80) cc_final: 0.8297 (t80) REVERT: 2 111 ASP cc_start: 0.6659 (m-30) cc_final: 0.6089 (m-30) REVERT: 2 162 HIS cc_start: 0.6596 (m90) cc_final: 0.6262 (m-70) REVERT: 2 170 MET cc_start: 0.6997 (ppp) cc_final: 0.6796 (ppp) REVERT: 4 26 MET cc_start: 0.4494 (ptt) cc_final: 0.3509 (ptp) REVERT: 4 64 TYR cc_start: 0.7827 (p90) cc_final: 0.7422 (p90) REVERT: 4 201 MET cc_start: 0.1871 (pmm) cc_final: 0.1404 (ptm) outliers start: 10 outliers final: 5 residues processed: 623 average time/residue: 0.3005 time to fit residues: 290.3446 Evaluate side-chains 499 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 494 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 389 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 325 GLN J 135 ASN J 325 GLN L 85 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 ASN L 325 GLN N 166 GLN N 172 GLN N 325 GLN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN R 83 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 180 ASN R 212 ASN R 279 GLN R 325 GLN ** U 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 325 GLN Y 180 ASN ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 166 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 117 GLN ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.079522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.065053 restraints weight = 268236.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.066445 restraints weight = 205085.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.067558 restraints weight = 164586.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.068466 restraints weight = 136362.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.069172 restraints weight = 115952.355| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 41757 Z= 0.225 Angle : 0.854 14.231 56592 Z= 0.426 Chirality : 0.053 0.600 6512 Planarity : 0.006 0.080 7120 Dihedral : 20.272 173.592 6816 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.29 % Allowed : 6.54 % Favored : 93.17 % 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 are not related in a simple way. whole: -0.39 (0.11), residues: 5216 helix: 0.37 (0.11), residues: 2272 sheet: 0.60 (0.18), residues: 800 loop : -1.23 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 168 TYR 0.105 0.006 TYR P 102 PHE 0.031 0.003 PHE 0 216 TRP 0.014 0.002 TRP 0 289 HIS 0.014 0.002 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (41712) covalent geometry : angle 0.85401 / 0.43 (56592) hydrogen bonds : bond 0.04281 / 2.87 ( 1904) hydrogen bonds : angle 5.29298 / 3.96 ( 5472) Misc. bond : bond 0.01080 / 0.71 ( 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 645 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 633 time to evaluate : 1.583 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 64 TYR cc_start: 0.8716 (p90) cc_final: 0.8325 (p90) REVERT: A 162 HIS cc_start: 0.7227 (m-70) cc_final: 0.6958 (m170) REVERT: A 237 VAL cc_start: 0.8458 (p) cc_final: 0.8180 (p) REVERT: A 256 GLN cc_start: 0.9168 (pm20) cc_final: 0.8800 (pm20) REVERT: A 268 TYR cc_start: 0.8288 (t80) cc_final: 0.8027 (t80) REVERT: A 320 LYS cc_start: 0.9482 (ptpp) cc_final: 0.9272 (ptpp) REVERT: C 109 ASN cc_start: 0.7645 (t0) cc_final: 0.7376 (t0) REVERT: C 158 MET cc_start: 0.7201 (pmm) cc_final: 0.6995 (pmm) REVERT: C 174 LEU cc_start: 0.9066 (mt) cc_final: 0.8832 (mt) REVERT: C 222 LEU cc_start: 0.7867 (mt) cc_final: 0.7206 (mm) REVERT: F 148 LEU cc_start: 0.8572 (tt) cc_final: 0.8310 (mm) REVERT: F 189 ILE cc_start: 0.5087 (tt) cc_final: 0.4689 (mp) REVERT: F 254 PHE cc_start: 0.6756 (m-10) cc_final: 0.6334 (m-10) REVERT: H 197 LYS cc_start: 0.7752 (mptt) cc_final: 0.7491 (mmtm) REVERT: H 223 ASP cc_start: 0.6568 (p0) cc_final: 0.6256 (p0) REVERT: H 268 TYR cc_start: 0.6197 (t80) cc_final: 0.5936 (t80) REVERT: J 26 MET cc_start: 0.1994 (pmm) cc_final: 0.0904 (ppp) REVERT: J 64 TYR cc_start: 0.7010 (p90) cc_final: 0.6805 (p90) REVERT: J 74 LEU cc_start: 0.8096 (tp) cc_final: 0.7778 (mt) REVERT: J 192 ASN cc_start: 0.3205 (t0) cc_final: 0.3003 (t0) REVERT: J 197 LYS cc_start: 0.8221 (mmpt) cc_final: 0.7885 (mmtm) REVERT: J 259 PHE cc_start: 0.6616 (p90) cc_final: 0.6201 (p90) REVERT: L 31 HIS cc_start: 0.8366 (t-170) cc_final: 0.8006 (t-170) REVERT: L 62 GLU cc_start: 0.7994 (pt0) cc_final: 0.7564 (tp30) REVERT: L 125 LEU cc_start: 0.8737 (mm) cc_final: 0.8494 (mt) REVERT: L 143 ASP cc_start: 0.8526 (t0) cc_final: 0.8242 (t0) REVERT: L 158 MET cc_start: 0.6433 (mmp) cc_final: 0.5118 (mmp) REVERT: L 215 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8719 (mmtm) REVERT: L 254 PHE cc_start: 0.8746 (m-80) cc_final: 0.8203 (m-80) REVERT: L 256 GLN cc_start: 0.8556 (pp30) cc_final: 0.8064 (pp30) REVERT: L 290 TYR cc_start: 0.7845 (m-80) cc_final: 0.7423 (m-80) REVERT: N 27 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7716 (mtt180) REVERT: N 162 HIS cc_start: 0.7695 (m170) cc_final: 0.7436 (m170) REVERT: N 320 LYS cc_start: 0.9537 (ptpt) cc_final: 0.9309 (ptpt) REVERT: P 111 ASP cc_start: 0.7905 (m-30) cc_final: 0.7607 (m-30) REVERT: P 162 HIS cc_start: 0.7592 (m170) cc_final: 0.7106 (m170) REVERT: P 268 TYR cc_start: 0.8255 (t80) cc_final: 0.7991 (t80) REVERT: P 276 LEU cc_start: 0.9361 (mp) cc_final: 0.9148 (tp) REVERT: P 303 ASN cc_start: 0.9428 (m-40) cc_final: 0.9165 (t0) REVERT: R 26 MET cc_start: -0.0228 (ptt) cc_final: -0.0953 (pmm) REVERT: R 148 LEU cc_start: 0.8268 (mp) cc_final: 0.8037 (pt) REVERT: R 158 MET cc_start: 0.5449 (pmm) cc_final: 0.5049 (pmm) REVERT: U 13 LEU cc_start: 0.9274 (mt) cc_final: 0.8939 (pp) REVERT: U 26 MET cc_start: 0.1556 (ptt) cc_final: 0.0642 (pmm) REVERT: U 196 MET cc_start: 0.6188 (mmm) cc_final: 0.5973 (mmm) REVERT: U 268 TYR cc_start: 0.6571 (t80) cc_final: 0.6251 (t80) REVERT: W 290 TYR cc_start: 0.7573 (t80) cc_final: 0.7290 (t80) REVERT: W 314 ILE cc_start: 0.8977 (mp) cc_final: 0.8751 (mp) REVERT: Y 26 MET cc_start: 0.4245 (pmm) cc_final: 0.3584 (pmm) REVERT: Y 64 TYR cc_start: 0.7421 (p90) cc_final: 0.7147 (p90) REVERT: Y 125 LEU cc_start: 0.9343 (mm) cc_final: 0.8927 (mt) REVERT: Y 129 ASP cc_start: 0.8214 (t70) cc_final: 0.7830 (m-30) REVERT: D 27 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8281 (mtm-85) REVERT: D 30 ASP cc_start: 0.8898 (t70) cc_final: 0.8246 (t0) REVERT: D 126 GLU cc_start: 0.8722 (pt0) cc_final: 0.8214 (pp20) REVERT: D 151 LYS cc_start: 0.9470 (ptmm) cc_final: 0.9064 (tppt) REVERT: D 180 ASN cc_start: 0.9402 (m-40) cc_final: 0.8967 (p0) REVERT: D 190 PHE cc_start: 0.9542 (m-80) cc_final: 0.9094 (m-10) REVERT: D 268 TYR cc_start: 0.8454 (t80) cc_final: 0.7913 (t80) REVERT: D 306 LYS cc_start: 0.9620 (pptt) cc_final: 0.9385 (ptmm) REVERT: 0 81 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9002 (mm-30) REVERT: 0 158 MET cc_start: 0.7883 (pmm) cc_final: 0.7644 (pmm) REVERT: 0 162 HIS cc_start: 0.6801 (m170) cc_final: 0.6414 (m170) REVERT: 0 222 LEU cc_start: 0.8830 (mp) cc_final: 0.8107 (mm) REVERT: 0 268 TYR cc_start: 0.8438 (t80) cc_final: 0.8190 (t80) REVERT: 2 162 HIS cc_start: 0.7542 (m90) cc_final: 0.7155 (m-70) REVERT: 4 201 MET cc_start: 0.2065 (pmm) cc_final: 0.1504 (ptm) outliers start: 12 outliers final: 9 residues processed: 645 average time/residue: 0.2893 time to fit residues: 292.1819 Evaluate side-chains 529 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 520 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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: 40.0000 chunk 385 optimal weight: 0.6980 chunk 329 optimal weight: 6.9990 chunk 375 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 460 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 284 optimal weight: 0.0570 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 260 GLN A 303 ASN A 325 GLN C 279 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 212 ASN 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 325 GLN N 325 GLN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 HIS R 212 ASN R 279 GLN 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 325 GLN Y 172 GLN Y 325 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.081081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.066246 restraints weight = 259401.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.067742 restraints weight = 195930.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.068917 restraints weight = 155546.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.069836 restraints weight = 128005.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.070607 restraints weight = 108573.995| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41757 Z= 0.157 Angle : 0.757 11.175 56592 Z= 0.376 Chirality : 0.050 0.326 6512 Planarity : 0.005 0.110 7120 Dihedral : 20.244 179.620 6816 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % 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 are not related in a simple way. whole: -0.16 (0.11), residues: 5216 helix: 0.57 (0.11), residues: 2240 sheet: 0.67 (0.19), residues: 800 loop : -1.07 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 221 TYR 0.115 0.005 TYR F 102 PHE 0.020 0.002 PHE J 216 TRP 0.012 0.001 TRP A 289 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (41712) covalent geometry : angle 0.75695 / 0.38 (56592) hydrogen bonds : bond 0.03752 / 2.53 ( 1904) hydrogen bonds : angle 5.12519 / 3.81 ( 5472) Misc. bond : bond 0.01085 / 0.71 ( 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 609 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 608 time to evaluate : 1.555 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: A 3 GLU cc_start: 0.9143 (pm20) cc_final: 0.8938 (pm20) REVERT: A 64 TYR cc_start: 0.8735 (p90) cc_final: 0.8288 (p90) REVERT: A 130 MET cc_start: 0.8586 (ttp) cc_final: 0.8293 (ppp) REVERT: A 162 HIS cc_start: 0.7184 (m-70) cc_final: 0.6929 (m170) REVERT: A 183 ASN cc_start: 0.9050 (m110) cc_final: 0.8805 (m-40) REVERT: A 190 PHE cc_start: 0.8999 (m-80) cc_final: 0.8799 (m-10) REVERT: A 256 GLN cc_start: 0.9103 (pm20) cc_final: 0.8717 (pp30) REVERT: A 268 TYR cc_start: 0.8428 (t80) cc_final: 0.8216 (t80) REVERT: A 320 LYS cc_start: 0.9520 (ptpp) cc_final: 0.9294 (ptpp) REVERT: C 109 ASN cc_start: 0.7734 (t0) cc_final: 0.7483 (t0) REVERT: C 143 ASP cc_start: 0.6805 (t0) cc_final: 0.6520 (t0) REVERT: C 180 ASN cc_start: 0.8731 (m-40) cc_final: 0.8412 (t0) REVERT: C 222 LEU cc_start: 0.7837 (mt) cc_final: 0.7154 (mm) REVERT: F 98 LEU cc_start: 0.7213 (pt) cc_final: 0.6977 (pt) REVERT: F 148 LEU cc_start: 0.8524 (tt) cc_final: 0.8232 (mm) REVERT: F 254 PHE cc_start: 0.6471 (m-10) cc_final: 0.6020 (m-10) REVERT: H 26 MET cc_start: 0.0744 (ptt) cc_final: 0.0540 (ptt) REVERT: H 197 LYS cc_start: 0.7614 (mptt) cc_final: 0.7383 (mmtm) REVERT: H 268 TYR cc_start: 0.5978 (t80) cc_final: 0.5604 (t80) REVERT: H 301 LYS cc_start: 0.7229 (tptt) cc_final: 0.6871 (tptt) REVERT: J 26 MET cc_start: 0.1648 (pmm) cc_final: 0.0571 (ppp) REVERT: J 74 LEU cc_start: 0.8025 (tp) cc_final: 0.7734 (mt) REVERT: J 192 ASN cc_start: 0.2743 (t0) cc_final: 0.2330 (t0) REVERT: J 244 LYS cc_start: 0.8067 (tttt) cc_final: 0.7739 (tptp) REVERT: L 26 MET cc_start: 0.4679 (pmm) cc_final: 0.2511 (ppp) REVERT: L 143 ASP cc_start: 0.8657 (t0) cc_final: 0.8279 (t0) REVERT: L 158 MET cc_start: 0.5415 (mmp) cc_final: 0.4645 (mmp) REVERT: L 221 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7349 (ttm110) REVERT: L 242 ARG cc_start: 0.8737 (ttt-90) cc_final: 0.7930 (ttp80) REVERT: L 254 PHE cc_start: 0.8605 (m-80) cc_final: 0.8224 (m-80) REVERT: L 256 GLN cc_start: 0.8478 (pp30) cc_final: 0.8040 (pp30) REVERT: N 151 LYS cc_start: 0.9086 (ptpp) cc_final: 0.8565 (pttm) REVERT: N 162 HIS cc_start: 0.7660 (m170) cc_final: 0.7444 (m170) REVERT: N 320 LYS cc_start: 0.9526 (ptpt) cc_final: 0.9293 (ptpt) REVERT: P 28 MET cc_start: 0.5340 (mmp) cc_final: 0.4975 (mmp) REVERT: P 112 ASP cc_start: 0.8431 (m-30) cc_final: 0.8101 (t0) REVERT: P 162 HIS cc_start: 0.7567 (m170) cc_final: 0.7147 (m170) REVERT: P 222 LEU cc_start: 0.8118 (mp) cc_final: 0.7808 (mt) REVERT: P 268 TYR cc_start: 0.8320 (t80) cc_final: 0.8069 (t80) REVERT: P 276 LEU cc_start: 0.9348 (mp) cc_final: 0.9144 (tp) REVERT: P 303 ASN cc_start: 0.9436 (m-40) cc_final: 0.9151 (t0) REVERT: R 148 LEU cc_start: 0.8155 (mp) cc_final: 0.7882 (pt) REVERT: R 158 MET cc_start: 0.4044 (pmm) cc_final: 0.3612 (pmm) REVERT: R 162 HIS cc_start: 0.8190 (m90) cc_final: 0.7952 (m-70) REVERT: R 191 ILE cc_start: 0.5398 (mm) cc_final: 0.5187 (mm) REVERT: U 13 LEU cc_start: 0.9280 (mt) cc_final: 0.8618 (pp) REVERT: U 26 MET cc_start: 0.0707 (ptt) cc_final: 0.0057 (pmm) REVERT: U 268 TYR cc_start: 0.6199 (t80) cc_final: 0.5818 (t80) REVERT: W 5 LYS cc_start: 0.8517 (tptt) cc_final: 0.7923 (pttm) REVERT: W 290 TYR cc_start: 0.7644 (t80) cc_final: 0.7392 (t80) REVERT: Y 26 MET cc_start: 0.4197 (pmm) cc_final: 0.3394 (pmm) REVERT: Y 64 TYR cc_start: 0.7363 (p90) cc_final: 0.7089 (p90) REVERT: Y 125 LEU cc_start: 0.9365 (mm) cc_final: 0.8936 (mt) REVERT: Y 129 ASP cc_start: 0.8201 (t70) cc_final: 0.7857 (m-30) REVERT: Y 158 MET cc_start: 0.8326 (mmp) cc_final: 0.7263 (mmp) REVERT: D 27 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8087 (mtm-85) REVERT: D 30 ASP cc_start: 0.8712 (t70) cc_final: 0.8148 (t0) REVERT: D 91 PHE cc_start: 0.9090 (t80) cc_final: 0.8887 (t80) REVERT: D 105 LYS cc_start: 0.9576 (ptpt) cc_final: 0.9332 (pttm) REVERT: D 126 GLU cc_start: 0.8719 (pt0) cc_final: 0.8195 (pp20) REVERT: D 155 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8908 (mm-30) REVERT: D 158 MET cc_start: 0.8192 (ptt) cc_final: 0.7395 (ptt) REVERT: D 180 ASN cc_start: 0.9353 (m-40) cc_final: 0.8889 (p0) REVERT: D 190 PHE cc_start: 0.9518 (m-80) cc_final: 0.9168 (m-10) REVERT: D 268 TYR cc_start: 0.8484 (t80) cc_final: 0.7886 (t80) REVERT: 0 81 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8938 (mm-30) REVERT: 0 91 PHE cc_start: 0.8778 (t80) cc_final: 0.8526 (t80) REVERT: 0 158 MET cc_start: 0.7552 (pmm) cc_final: 0.7133 (pmm) REVERT: 0 162 HIS cc_start: 0.7113 (m170) cc_final: 0.6713 (m170) REVERT: 0 222 LEU cc_start: 0.8670 (mp) cc_final: 0.8026 (mm) REVERT: 0 254 PHE cc_start: 0.9571 (m-10) cc_final: 0.9359 (m-80) REVERT: 2 111 ASP cc_start: 0.7025 (m-30) cc_final: 0.6448 (m-30) REVERT: 2 145 VAL cc_start: 0.6906 (t) cc_final: 0.6588 (t) REVERT: 2 162 HIS cc_start: 0.7561 (m90) cc_final: 0.7203 (m-70) REVERT: 2 189 ILE cc_start: 0.6447 (tp) cc_final: 0.6229 (tp) REVERT: 4 26 MET cc_start: 0.4981 (ptt) cc_final: 0.3769 (pmm) REVERT: 4 201 MET cc_start: 0.2104 (pmm) cc_final: 0.1796 (ptm) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.2930 time to fit residues: 279.6388 Evaluate side-chains 473 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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: 0.9980 chunk 118 optimal weight: 7.9990 chunk 385 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 398 optimal weight: 5.9990 chunk 472 optimal weight: 7.9990 chunk 419 optimal weight: 0.0370 chunk 506 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 505 optimal weight: 6.9990 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 279 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 325 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 279 GLN 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 162 HIS ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.079035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064203 restraints weight = 263597.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.065687 restraints weight = 198850.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.066904 restraints weight = 157897.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.067874 restraints weight = 129428.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.068660 restraints weight = 108987.517| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.8191 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= 0.166 Angle : 0.745 9.996 56592 Z= 0.373 Chirality : 0.048 0.277 6512 Planarity : 0.005 0.089 7120 Dihedral : 20.245 179.134 6816 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 are not related in a simple way. whole: -0.11 (0.12), residues: 5216 helix: 0.63 (0.11), residues: 2240 sheet: 0.72 (0.19), residues: 784 loop : -1.08 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 221 TYR 0.122 0.006 TYR N 102 PHE 0.023 0.002 PHE F 216 TRP 0.031 0.001 TRP N 289 HIS 0.006 0.001 HIS J 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (41712) covalent geometry : angle 0.74480 / 0.37 (56592) hydrogen bonds : bond 0.03695 / 2.49 ( 1904) hydrogen bonds : angle 5.09047 / 3.79 ( 5472) Misc. bond : bond 0.01128 / 0.74 ( 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 595 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.570 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: 0.8805 (p90) cc_final: 0.8389 (p90) REVERT: A 183 ASN cc_start: 0.9014 (m110) cc_final: 0.8768 (m-40) REVERT: A 237 VAL cc_start: 0.8485 (p) cc_final: 0.8265 (p) REVERT: A 256 GLN cc_start: 0.9170 (pm20) cc_final: 0.8776 (pp30) REVERT: A 268 TYR cc_start: 0.8481 (t80) cc_final: 0.8274 (t80) REVERT: A 306 LYS cc_start: 0.9425 (ptpp) cc_final: 0.9206 (pttm) REVERT: A 320 LYS cc_start: 0.9510 (ptpp) cc_final: 0.9268 (ptpp) REVERT: C 109 ASN cc_start: 0.7812 (t0) cc_final: 0.7532 (t0) REVERT: C 130 MET cc_start: 0.8478 (ttp) cc_final: 0.7056 (ttt) REVERT: C 158 MET cc_start: 0.7402 (pmm) cc_final: 0.7104 (pmm) REVERT: C 222 LEU cc_start: 0.7915 (mt) cc_final: 0.7246 (mm) REVERT: F 26 MET cc_start: -0.0403 (ptp) cc_final: -0.0749 (ptp) REVERT: F 98 LEU cc_start: 0.7549 (pt) cc_final: 0.7298 (pt) REVERT: F 109 ASN cc_start: 0.7187 (t0) cc_final: 0.6854 (t0) REVERT: F 148 LEU cc_start: 0.8547 (tt) cc_final: 0.8262 (mm) REVERT: F 189 ILE cc_start: 0.5267 (tt) cc_final: 0.4760 (mp) REVERT: F 220 VAL cc_start: 0.4829 (p) cc_final: 0.4014 (p) REVERT: F 254 PHE cc_start: 0.6815 (m-10) cc_final: 0.6294 (m-10) REVERT: F 269 ARG cc_start: 0.8363 (mpp-170) cc_final: 0.7992 (mpt-90) REVERT: H 197 LYS cc_start: 0.7579 (mptt) cc_final: 0.7337 (mmtm) REVERT: H 268 TYR cc_start: 0.6139 (t80) cc_final: 0.5695 (t80) REVERT: H 301 LYS cc_start: 0.7415 (tptt) cc_final: 0.6999 (tptt) REVERT: J 15 GLN cc_start: 0.9309 (tt0) cc_final: 0.8972 (tm-30) REVERT: J 16 ILE cc_start: 0.8800 (tp) cc_final: 0.8028 (tp) REVERT: J 26 MET cc_start: 0.1754 (pmm) cc_final: 0.1026 (ppp) REVERT: J 74 LEU cc_start: 0.8156 (tp) cc_final: 0.7842 (mt) REVERT: J 192 ASN cc_start: 0.2638 (t0) cc_final: 0.2193 (t0) REVERT: J 244 LYS cc_start: 0.8165 (tttt) cc_final: 0.7794 (tptp) REVERT: J 259 PHE cc_start: 0.6877 (p90) cc_final: 0.6574 (p90) REVERT: L 26 MET cc_start: 0.4817 (pmm) cc_final: 0.2535 (ppp) REVERT: L 143 ASP cc_start: 0.8612 (t0) cc_final: 0.8226 (t0) REVERT: L 221 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7545 (ttm110) REVERT: L 242 ARG cc_start: 0.8709 (ttt-90) cc_final: 0.7925 (ttp80) REVERT: L 254 PHE cc_start: 0.8725 (m-80) cc_final: 0.8359 (m-80) REVERT: L 256 GLN cc_start: 0.8506 (pp30) cc_final: 0.8053 (pp30) REVERT: N 151 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8656 (ptpp) REVERT: N 162 HIS cc_start: 0.7515 (m170) cc_final: 0.7097 (m170) REVERT: N 320 LYS cc_start: 0.9534 (ptpt) cc_final: 0.9303 (ptpt) REVERT: P 28 MET cc_start: 0.4965 (mmp) cc_final: 0.4604 (mmp) REVERT: P 112 ASP cc_start: 0.8547 (m-30) cc_final: 0.8166 (t0) REVERT: P 151 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8866 (mmtm) REVERT: P 268 TYR cc_start: 0.8288 (t80) cc_final: 0.8029 (t80) REVERT: P 303 ASN cc_start: 0.9378 (m-40) cc_final: 0.9137 (t0) REVERT: R 133 ARG cc_start: 0.8266 (ptp-110) cc_final: 0.7993 (ptp-110) REVERT: R 148 LEU cc_start: 0.8154 (mp) cc_final: 0.7941 (pt) REVERT: R 151 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8255 (mmmt) REVERT: R 158 MET cc_start: 0.4303 (pmm) cc_final: 0.3814 (pmm) REVERT: R 162 HIS cc_start: 0.8386 (m90) cc_final: 0.8111 (m-70) REVERT: U 13 LEU cc_start: 0.9263 (mt) cc_final: 0.8680 (pp) REVERT: U 26 MET cc_start: 0.1008 (ptt) cc_final: 0.0390 (pmm) REVERT: U 268 TYR cc_start: 0.6413 (t80) cc_final: 0.6072 (t80) REVERT: W 112 ASP cc_start: 0.7522 (m-30) cc_final: 0.7111 (t0) REVERT: W 290 TYR cc_start: 0.7593 (t80) cc_final: 0.7311 (t80) REVERT: Y 26 MET cc_start: 0.4198 (pmm) cc_final: 0.3432 (pmm) REVERT: Y 64 TYR cc_start: 0.7460 (p90) cc_final: 0.7174 (p90) REVERT: Y 129 ASP cc_start: 0.8260 (t70) cc_final: 0.7889 (m-30) REVERT: Y 207 THR cc_start: 0.8986 (p) cc_final: 0.8618 (p) REVERT: Y 225 ARG cc_start: 0.8096 (mmm160) cc_final: 0.6840 (mmm-85) REVERT: Y 254 PHE cc_start: 0.8571 (m-80) cc_final: 0.8320 (m-80) REVERT: D 126 GLU cc_start: 0.8656 (pt0) cc_final: 0.8200 (pp20) REVERT: D 130 MET cc_start: 0.8932 (ppp) cc_final: 0.8663 (ppp) REVERT: D 155 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8902 (mm-30) REVERT: D 162 HIS cc_start: 0.7320 (m90) cc_final: 0.7049 (m170) REVERT: D 180 ASN cc_start: 0.9342 (m-40) cc_final: 0.8860 (p0) REVERT: D 190 PHE cc_start: 0.9520 (m-80) cc_final: 0.9184 (m-10) REVERT: D 268 TYR cc_start: 0.8458 (t80) cc_final: 0.7873 (t80) REVERT: D 289 TRP cc_start: 0.8543 (m100) cc_final: 0.8059 (m100) REVERT: 0 91 PHE cc_start: 0.8896 (t80) cc_final: 0.8611 (t80) REVERT: 0 158 MET cc_start: 0.7647 (pmm) cc_final: 0.7230 (pmm) REVERT: 0 162 HIS cc_start: 0.7173 (m170) cc_final: 0.6719 (m170) REVERT: 0 222 LEU cc_start: 0.8801 (mp) cc_final: 0.8149 (mm) REVERT: 0 254 PHE cc_start: 0.9602 (m-10) cc_final: 0.9384 (m-80) REVERT: 2 145 VAL cc_start: 0.6932 (t) cc_final: 0.6619 (t) REVERT: 2 162 HIS cc_start: 0.7541 (m90) cc_final: 0.7234 (m-70) REVERT: 2 189 ILE cc_start: 0.6239 (tp) cc_final: 0.6021 (tp) REVERT: 4 201 MET cc_start: 0.2023 (pmm) cc_final: 0.1672 (ptm) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2950 time to fit residues: 273.9858 Evaluate side-chains 474 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 345 optimal weight: 1.9990 chunk 356 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 495 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 337 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 279 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS F 325 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 325 GLN P 279 GLN P 325 GLN R 212 ASN R 279 GLN 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 279 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.080640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.065785 restraints weight = 256790.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067212 restraints weight = 194967.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.068384 restraints weight = 155998.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.069313 restraints weight = 128970.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.070019 restraints weight = 109728.834| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41757 Z= 0.151 Angle : 0.730 8.939 56592 Z= 0.366 Chirality : 0.048 0.244 6512 Planarity : 0.005 0.078 7120 Dihedral : 20.313 179.951 6816 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 5216 helix: 0.65 (0.11), residues: 2240 sheet: 0.72 (0.19), residues: 784 loop : -1.08 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG 0 242 TYR 0.116 0.005 TYR Y 102 PHE 0.022 0.002 PHE 0 216 TRP 0.008 0.001 TRP C 289 HIS 0.004 0.001 HIS 0 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (41712) covalent geometry : angle 0.73012 / 0.37 (56592) hydrogen bonds : bond 0.03673 / 2.51 ( 1904) hydrogen bonds : angle 5.08861 / 3.77 ( 5472) Misc. bond : bond 0.01078 / 0.68 ( 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 : 1.590 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 64 TYR cc_start: 0.8710 (p90) cc_final: 0.8292 (p90) REVERT: A 183 ASN cc_start: 0.8987 (m110) cc_final: 0.8745 (m-40) REVERT: A 256 GLN cc_start: 0.9148 (pm20) cc_final: 0.8795 (pp30) REVERT: A 320 LYS cc_start: 0.9540 (ptpp) cc_final: 0.9320 (ptpp) REVERT: C 109 ASN cc_start: 0.7781 (t0) cc_final: 0.7547 (t0) REVERT: C 130 MET cc_start: 0.8240 (ttp) cc_final: 0.7640 (ttt) REVERT: C 158 MET cc_start: 0.7463 (pmm) cc_final: 0.7155 (pmm) REVERT: C 222 LEU cc_start: 0.8047 (mt) cc_final: 0.7386 (mm) REVERT: F 98 LEU cc_start: 0.7649 (pt) cc_final: 0.7359 (pt) REVERT: F 109 ASN cc_start: 0.7230 (t0) cc_final: 0.6916 (t0) REVERT: F 148 LEU cc_start: 0.8497 (tt) cc_final: 0.8214 (mm) REVERT: F 254 PHE cc_start: 0.6598 (m-10) cc_final: 0.6085 (m-10) REVERT: H 197 LYS cc_start: 0.7672 (mptt) cc_final: 0.7405 (mmtm) REVERT: H 242 ARG cc_start: 0.7628 (tmt170) cc_final: 0.7358 (ttp80) REVERT: H 244 LYS cc_start: 0.7914 (tmtt) cc_final: 0.7702 (tmtt) REVERT: H 291 SER cc_start: 0.4013 (m) cc_final: 0.3812 (m) REVERT: J 15 GLN cc_start: 0.9334 (tt0) cc_final: 0.8801 (tm-30) REVERT: J 16 ILE cc_start: 0.8853 (tp) cc_final: 0.8121 (tp) REVERT: J 122 GLU cc_start: 0.8769 (pm20) cc_final: 0.8369 (pm20) REVERT: J 307 TYR cc_start: 0.7275 (m-80) cc_final: 0.7066 (m-10) REVERT: L 26 MET cc_start: 0.4712 (pmm) cc_final: 0.2484 (ppp) REVERT: L 143 ASP cc_start: 0.8522 (t0) cc_final: 0.8153 (t0) REVERT: L 221 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7553 (ttm110) REVERT: L 242 ARG cc_start: 0.8766 (ttt-90) cc_final: 0.7982 (ttp80) REVERT: L 254 PHE cc_start: 0.8694 (m-80) cc_final: 0.8314 (m-80) REVERT: L 256 GLN cc_start: 0.8580 (pp30) cc_final: 0.8079 (pp30) REVERT: N 320 LYS cc_start: 0.9531 (ptpt) cc_final: 0.9300 (ptpt) REVERT: P 28 MET cc_start: 0.4869 (mmp) cc_final: 0.4578 (mmp) REVERT: P 112 ASP cc_start: 0.8555 (m-30) cc_final: 0.8151 (t0) REVERT: P 268 TYR cc_start: 0.8289 (t80) cc_final: 0.7979 (t80) REVERT: P 303 ASN cc_start: 0.9422 (m-40) cc_final: 0.9153 (t0) REVERT: R 133 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.8044 (ptp-110) REVERT: R 148 LEU cc_start: 0.8166 (mp) cc_final: 0.7965 (pt) REVERT: R 162 HIS cc_start: 0.8476 (m90) cc_final: 0.8223 (m-70) REVERT: U 13 LEU cc_start: 0.9237 (mt) cc_final: 0.9011 (pp) REVERT: U 26 MET cc_start: 0.0754 (ptt) cc_final: 0.0260 (pmm) REVERT: U 162 HIS cc_start: 0.7903 (m90) cc_final: 0.7530 (m170) REVERT: U 216 PHE cc_start: 0.2713 (m-10) cc_final: 0.2372 (m-80) REVERT: U 268 TYR cc_start: 0.6322 (t80) cc_final: 0.5879 (t80) REVERT: W 5 LYS cc_start: 0.8633 (tptt) cc_final: 0.8014 (pttm) REVERT: W 112 ASP cc_start: 0.7536 (m-30) cc_final: 0.7133 (t0) REVERT: W 290 TYR cc_start: 0.7719 (t80) cc_final: 0.7453 (t80) REVERT: Y 26 MET cc_start: 0.4089 (pmm) cc_final: 0.3268 (pmm) REVERT: Y 129 ASP cc_start: 0.8279 (t70) cc_final: 0.7928 (m-30) REVERT: Y 178 THR cc_start: 0.8488 (t) cc_final: 0.8090 (p) REVERT: Y 225 ARG cc_start: 0.7398 (mmm160) cc_final: 0.6901 (mmm-85) REVERT: D 91 PHE cc_start: 0.9086 (t80) cc_final: 0.8870 (t80) REVERT: D 105 LYS cc_start: 0.9577 (ptpt) cc_final: 0.9339 (pttm) REVERT: D 126 GLU cc_start: 0.8779 (pt0) cc_final: 0.8222 (pp20) REVERT: D 130 MET cc_start: 0.8974 (ppp) cc_final: 0.8747 (ppp) REVERT: D 155 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8886 (mm-30) REVERT: D 162 HIS cc_start: 0.7566 (m90) cc_final: 0.7134 (m170) REVERT: D 180 ASN cc_start: 0.9320 (m-40) cc_final: 0.8811 (p0) REVERT: D 190 PHE cc_start: 0.9513 (m-80) cc_final: 0.9180 (m-10) REVERT: D 268 TYR cc_start: 0.8406 (t80) cc_final: 0.7872 (t80) REVERT: D 320 LYS cc_start: 0.9557 (ptpp) cc_final: 0.9355 (pttm) REVERT: 0 91 PHE cc_start: 0.8897 (t80) cc_final: 0.8593 (t80) REVERT: 0 148 LEU cc_start: 0.9229 (tp) cc_final: 0.8907 (tp) REVERT: 0 158 MET cc_start: 0.7556 (pmm) cc_final: 0.7141 (pmm) REVERT: 0 162 HIS cc_start: 0.7178 (m170) cc_final: 0.6716 (m170) REVERT: 0 208 THR cc_start: 0.8424 (t) cc_final: 0.8212 (m) REVERT: 0 222 LEU cc_start: 0.8683 (mp) cc_final: 0.8078 (mm) REVERT: 0 254 PHE cc_start: 0.9575 (m-10) cc_final: 0.9343 (m-80) REVERT: 0 268 TYR cc_start: 0.8462 (t80) cc_final: 0.8087 (t80) REVERT: 2 111 ASP cc_start: 0.7142 (m-30) cc_final: 0.6607 (m-30) REVERT: 2 145 VAL cc_start: 0.6836 (t) cc_final: 0.6494 (t) REVERT: 2 162 HIS cc_start: 0.7630 (m90) cc_final: 0.7386 (m-70) REVERT: 2 189 ILE cc_start: 0.6243 (tp) cc_final: 0.6026 (tp) REVERT: 2 260 GLN cc_start: 0.5954 (mt0) cc_final: 0.5719 (mp10) REVERT: 4 26 MET cc_start: 0.4983 (ptt) cc_final: 0.3987 (pmm) REVERT: 4 196 MET cc_start: 0.2473 (mmm) cc_final: 0.2264 (tpp) REVERT: 4 201 MET cc_start: 0.1891 (pmm) cc_final: 0.1492 (ptm) outliers start: 1 outliers final: 1 residues processed: 594 average time/residue: 0.2978 time to fit residues: 276.9990 Evaluate side-chains 478 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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: 5.9990 chunk 407 optimal weight: 9.9990 chunk 73 optimal weight: 0.0370 chunk 58 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 418 optimal weight: 3.9990 chunk 425 optimal weight: 20.0000 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 325 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 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 325 GLN N 303 ASN N 325 GLN P 180 ASN P 279 GLN P 325 GLN R 212 ASN R 279 GLN R 325 GLN ** 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 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN 0 279 GLN ** 0 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064033 restraints weight = 264461.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.065469 restraints weight = 200863.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.066603 restraints weight = 159849.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.067533 restraints weight = 132186.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.068256 restraints weight = 111931.750| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 41757 Z= 0.163 Angle : 0.758 12.839 56592 Z= 0.380 Chirality : 0.048 0.231 6512 Planarity : 0.006 0.100 7120 Dihedral : 20.394 177.096 6816 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 are not related in a simple way. whole: -0.21 (0.12), residues: 5216 helix: 0.56 (0.11), residues: 2272 sheet: 0.65 (0.19), residues: 784 loop : -1.15 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 175 TYR 0.110 0.005 TYR P 102 PHE 0.023 0.002 PHE Y 91 TRP 0.007 0.001 TRP D 289 HIS 0.007 0.001 HIS Y 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (41712) covalent geometry : angle 0.75773 / 0.38 (56592) hydrogen bonds : bond 0.03754 / 2.56 ( 1904) hydrogen bonds : angle 5.12202 / 3.80 ( 5472) Misc. bond : bond 0.01067 / 0.68 ( 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 596 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.664 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 64 TYR cc_start: 0.8730 (p90) cc_final: 0.8303 (p90) REVERT: A 183 ASN cc_start: 0.8954 (m110) cc_final: 0.8709 (m-40) REVERT: A 256 GLN cc_start: 0.9159 (pm20) cc_final: 0.8734 (pp30) REVERT: A 320 LYS cc_start: 0.9524 (ptpp) cc_final: 0.9297 (ptpp) REVERT: C 109 ASN cc_start: 0.7882 (t0) cc_final: 0.7670 (t0) REVERT: C 158 MET cc_start: 0.7627 (pmm) cc_final: 0.7335 (pmm) REVERT: C 222 LEU cc_start: 0.8178 (mt) cc_final: 0.7593 (mm) REVERT: C 256 GLN cc_start: 0.8546 (pm20) cc_final: 0.8329 (pm20) REVERT: F 98 LEU cc_start: 0.7983 (pt) cc_final: 0.7703 (pt) REVERT: F 109 ASN cc_start: 0.7294 (t0) cc_final: 0.6901 (t0) REVERT: F 148 LEU cc_start: 0.8637 (tt) cc_final: 0.8270 (mm) REVERT: F 254 PHE cc_start: 0.6893 (m-10) cc_final: 0.6692 (m-10) REVERT: H 197 LYS cc_start: 0.7645 (mptt) cc_final: 0.7380 (mmtm) REVERT: H 291 SER cc_start: 0.4155 (m) cc_final: 0.3940 (m) REVERT: J 15 GLN cc_start: 0.9313 (tt0) cc_final: 0.8810 (tm-30) REVERT: J 16 ILE cc_start: 0.8742 (tp) cc_final: 0.8130 (tp) REVERT: J 26 MET cc_start: 0.2487 (pmm) cc_final: 0.1209 (ppp) REVERT: J 64 TYR cc_start: 0.7235 (p90) cc_final: 0.6998 (p90) REVERT: J 122 GLU cc_start: 0.8757 (pm20) cc_final: 0.8505 (pm20) REVERT: J 158 MET cc_start: 0.7840 (mpp) cc_final: 0.7540 (mpp) REVERT: J 307 TYR cc_start: 0.7449 (m-80) cc_final: 0.7218 (m-10) REVERT: L 143 ASP cc_start: 0.8404 (t0) cc_final: 0.8073 (t0) REVERT: L 206 GLU cc_start: 0.8123 (mp0) cc_final: 0.7648 (pm20) REVERT: L 242 ARG cc_start: 0.8737 (ttt-90) cc_final: 0.8040 (ttp80) REVERT: L 254 PHE cc_start: 0.8760 (m-80) cc_final: 0.8476 (m-80) REVERT: L 256 GLN cc_start: 0.8685 (pp30) cc_final: 0.8315 (pp30) REVERT: N 151 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8817 (ptpp) REVERT: N 162 HIS cc_start: 0.7549 (m170) cc_final: 0.7158 (m170) REVERT: N 235 GLU cc_start: 0.8692 (pp20) cc_final: 0.8374 (pp20) REVERT: N 320 LYS cc_start: 0.9528 (ptpt) cc_final: 0.9305 (ptpt) REVERT: P 28 MET cc_start: 0.5010 (mmp) cc_final: 0.4712 (mmp) REVERT: P 111 ASP cc_start: 0.7951 (m-30) cc_final: 0.7720 (m-30) REVERT: P 112 ASP cc_start: 0.8609 (m-30) cc_final: 0.8230 (t0) REVERT: P 268 TYR cc_start: 0.8245 (t80) cc_final: 0.7983 (t80) REVERT: R 26 MET cc_start: -0.0250 (ptt) cc_final: -0.0842 (pmm) REVERT: R 109 ASN cc_start: 0.7511 (t0) cc_final: 0.7184 (t0) REVERT: R 162 HIS cc_start: 0.8526 (m90) cc_final: 0.8317 (m-70) REVERT: U 13 LEU cc_start: 0.9221 (mt) cc_final: 0.8989 (pp) REVERT: U 26 MET cc_start: 0.1347 (ptt) cc_final: 0.1070 (pmm) REVERT: W 28 MET cc_start: 0.7484 (mmp) cc_final: 0.7195 (mmp) REVERT: W 112 ASP cc_start: 0.7838 (m-30) cc_final: 0.7272 (t0) REVERT: W 153 GLU cc_start: 0.5258 (mm-30) cc_final: 0.4790 (mm-30) REVERT: W 290 TYR cc_start: 0.7733 (t80) cc_final: 0.7405 (t80) REVERT: Y 26 MET cc_start: 0.4150 (pmm) cc_final: 0.3323 (pmm) REVERT: Y 178 THR cc_start: 0.8589 (t) cc_final: 0.8242 (p) REVERT: Y 206 GLU cc_start: 0.9076 (pm20) cc_final: 0.8742 (pm20) REVERT: Y 242 ARG cc_start: 0.8457 (ptt-90) cc_final: 0.7652 (mtm-85) REVERT: D 67 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8700 (mt-10) REVERT: D 91 PHE cc_start: 0.9102 (t80) cc_final: 0.8900 (t80) REVERT: D 126 GLU cc_start: 0.8742 (pt0) cc_final: 0.8303 (pp20) REVERT: D 130 MET cc_start: 0.9026 (ppp) cc_final: 0.8795 (ppp) REVERT: D 155 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8888 (mm-30) REVERT: D 162 HIS cc_start: 0.7606 (m90) cc_final: 0.7225 (m170) REVERT: D 180 ASN cc_start: 0.9332 (m-40) cc_final: 0.8831 (p0) REVERT: D 190 PHE cc_start: 0.9523 (m-80) cc_final: 0.9201 (m-10) REVERT: D 268 TYR cc_start: 0.8391 (t80) cc_final: 0.7862 (t80) REVERT: D 289 TRP cc_start: 0.8479 (m100) cc_final: 0.7981 (m100) REVERT: D 320 LYS cc_start: 0.9557 (ptpp) cc_final: 0.9352 (pttm) REVERT: 0 91 PHE cc_start: 0.9015 (t80) cc_final: 0.8671 (t80) REVERT: 0 158 MET cc_start: 0.7336 (pmm) cc_final: 0.6943 (pmm) REVERT: 0 162 HIS cc_start: 0.7201 (m170) cc_final: 0.6747 (m170) REVERT: 0 254 PHE cc_start: 0.9592 (m-10) cc_final: 0.9387 (m-80) REVERT: 0 268 TYR cc_start: 0.8418 (t80) cc_final: 0.8107 (t80) REVERT: 2 145 VAL cc_start: 0.6992 (t) cc_final: 0.6694 (t) REVERT: 2 260 GLN cc_start: 0.5976 (mt0) cc_final: 0.5711 (mp10) REVERT: 4 201 MET cc_start: 0.1963 (pmm) cc_final: 0.1614 (ptm) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.2977 time to fit residues: 277.0671 Evaluate side-chains 491 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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: 1.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 416 optimal weight: 0.0870 chunk 328 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 447 optimal weight: 0.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 325 GLN C 279 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 ** 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 325 GLN ** N 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 303 ASN N 325 GLN P 279 GLN P 325 GLN R 212 ASN R 279 GLN 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 325 GLN D 279 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 162 HIS ** 4 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.077925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.063320 restraints weight = 262348.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.064760 restraints weight = 198001.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.065910 restraints weight = 157549.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.066788 restraints weight = 129806.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.067524 restraints weight = 110665.906| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.9532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41757 Z= 0.161 Angle : 0.759 13.147 56592 Z= 0.380 Chirality : 0.048 0.237 6512 Planarity : 0.006 0.106 7120 Dihedral : 20.374 176.131 6816 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.02 % Allowed : 0.78 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 5216 helix: 0.56 (0.11), residues: 2272 sheet: 0.51 (0.19), residues: 800 loop : -1.18 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 168 TYR 0.108 0.005 TYR P 102 PHE 0.023 0.001 PHE H 216 TRP 0.019 0.001 TRP Y 289 HIS 0.010 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (41712) covalent geometry : angle 0.75854 / 0.38 (56592) hydrogen bonds : bond 0.03702 / 2.51 ( 1904) hydrogen bonds : angle 5.15553 / 3.81 ( 5472) Misc. bond : bond 0.01035 / 0.66 ( 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 591 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 1.605 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: A 64 TYR cc_start: 0.8839 (p90) cc_final: 0.8447 (p90) REVERT: A 91 PHE cc_start: 0.8422 (t80) cc_final: 0.8177 (t80) REVERT: A 183 ASN cc_start: 0.8965 (m110) cc_final: 0.8733 (m-40) REVERT: A 215 LYS cc_start: 0.9604 (ptpp) cc_final: 0.9270 (tmtt) REVERT: A 256 GLN cc_start: 0.9140 (pm20) cc_final: 0.8849 (pp30) REVERT: A 268 TYR cc_start: 0.8502 (t80) cc_final: 0.8211 (t80) REVERT: A 306 LYS cc_start: 0.9491 (ptpp) cc_final: 0.9253 (pttm) REVERT: A 320 LYS cc_start: 0.9550 (ptpp) cc_final: 0.9341 (ptpp) REVERT: C 130 MET cc_start: 0.8220 (ttp) cc_final: 0.7869 (ptm) REVERT: C 151 LYS cc_start: 0.9019 (mmpt) cc_final: 0.8803 (mmmt) REVERT: C 158 MET cc_start: 0.7703 (pmm) cc_final: 0.7429 (pmm) REVERT: C 183 ASN cc_start: 0.9258 (m110) cc_final: 0.9054 (m-40) REVERT: C 222 LEU cc_start: 0.8266 (mt) cc_final: 0.7702 (mm) REVERT: C 256 GLN cc_start: 0.8683 (pm20) cc_final: 0.8435 (pm20) REVERT: F 109 ASN cc_start: 0.7302 (t0) cc_final: 0.6891 (t0) REVERT: F 148 LEU cc_start: 0.8693 (tt) cc_final: 0.8329 (mm) REVERT: F 254 PHE cc_start: 0.7136 (m-10) cc_final: 0.6885 (m-10) REVERT: H 109 ASN cc_start: 0.6387 (t0) cc_final: 0.6027 (t0) REVERT: H 197 LYS cc_start: 0.7780 (mptt) cc_final: 0.7445 (mmtm) REVERT: J 15 GLN cc_start: 0.9266 (tt0) cc_final: 0.8814 (tm-30) REVERT: J 16 ILE cc_start: 0.8843 (tp) cc_final: 0.8159 (tp) REVERT: J 26 MET cc_start: 0.2805 (pmm) cc_final: 0.2101 (pmm) REVERT: J 64 TYR cc_start: 0.7276 (p90) cc_final: 0.6969 (p90) REVERT: J 122 GLU cc_start: 0.8869 (pm20) cc_final: 0.8532 (pm20) REVERT: J 158 MET cc_start: 0.8006 (mpp) cc_final: 0.7718 (mpp) REVERT: J 259 PHE cc_start: 0.7394 (p90) cc_final: 0.7047 (p90) REVERT: J 307 TYR cc_start: 0.7520 (m-80) cc_final: 0.7277 (m-10) REVERT: L 26 MET cc_start: 0.4490 (pmm) cc_final: 0.2567 (ppp) REVERT: L 126 GLU cc_start: 0.8796 (pt0) cc_final: 0.8333 (pp20) REVERT: L 143 ASP cc_start: 0.8438 (t0) cc_final: 0.8157 (t0) REVERT: L 242 ARG cc_start: 0.8801 (ttt-90) cc_final: 0.8101 (ttp80) REVERT: L 254 PHE cc_start: 0.8791 (m-80) cc_final: 0.8470 (m-80) REVERT: L 256 GLN cc_start: 0.8708 (pp30) cc_final: 0.8304 (pp30) REVERT: N 151 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8834 (ptpp) REVERT: N 235 GLU cc_start: 0.8736 (pp20) cc_final: 0.8455 (pp20) REVERT: N 290 TYR cc_start: 0.9051 (m-80) cc_final: 0.8842 (m-10) REVERT: N 320 LYS cc_start: 0.9533 (ptpt) cc_final: 0.9319 (ptpt) REVERT: P 112 ASP cc_start: 0.8651 (m-30) cc_final: 0.8324 (t0) REVERT: P 268 TYR cc_start: 0.8307 (t80) cc_final: 0.8035 (t80) REVERT: R 26 MET cc_start: -0.0379 (ptt) cc_final: -0.0914 (pmm) REVERT: R 109 ASN cc_start: 0.7509 (t0) cc_final: 0.7185 (t0) REVERT: R 135 ASN cc_start: 0.8412 (m-40) cc_final: 0.8101 (m110) REVERT: R 162 HIS cc_start: 0.8597 (m90) cc_final: 0.8326 (m170) REVERT: U 13 LEU cc_start: 0.9269 (mt) cc_final: 0.9002 (pp) REVERT: U 26 MET cc_start: 0.1541 (ptt) cc_final: 0.1183 (pmm) REVERT: U 109 ASN cc_start: 0.6324 (t0) cc_final: 0.5970 (t0) REVERT: U 190 PHE cc_start: 0.4913 (t80) cc_final: 0.4609 (t80) REVERT: W 5 LYS cc_start: 0.8696 (tptt) cc_final: 0.8136 (pttm) REVERT: W 112 ASP cc_start: 0.8023 (m-30) cc_final: 0.7374 (t0) REVERT: W 153 GLU cc_start: 0.5659 (mm-30) cc_final: 0.5179 (mm-30) REVERT: W 240 GLU cc_start: 0.7302 (pm20) cc_final: 0.6910 (pm20) REVERT: W 290 TYR cc_start: 0.7756 (t80) cc_final: 0.7471 (t80) REVERT: W 320 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9120 (mttt) REVERT: Y 26 MET cc_start: 0.4110 (pmm) cc_final: 0.3237 (pmm) REVERT: Y 129 ASP cc_start: 0.8448 (t70) cc_final: 0.8154 (t0) REVERT: Y 178 THR cc_start: 0.8703 (t) cc_final: 0.8402 (p) REVERT: Y 206 GLU cc_start: 0.9132 (pm20) cc_final: 0.8781 (pm20) REVERT: D 67 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8799 (mt-10) REVERT: D 91 PHE cc_start: 0.9089 (t80) cc_final: 0.8869 (t80) REVERT: D 126 GLU cc_start: 0.8894 (pt0) cc_final: 0.8275 (pp20) REVERT: D 130 MET cc_start: 0.9061 (ppp) cc_final: 0.8838 (ppp) REVERT: D 155 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8864 (mm-30) REVERT: D 162 HIS cc_start: 0.7544 (m90) cc_final: 0.7153 (m170) REVERT: D 180 ASN cc_start: 0.9319 (m-40) cc_final: 0.8816 (p0) REVERT: D 242 ARG cc_start: 0.8850 (pmt170) cc_final: 0.8574 (ptt-90) REVERT: D 268 TYR cc_start: 0.8426 (t80) cc_final: 0.7912 (t80) REVERT: D 289 TRP cc_start: 0.8479 (m100) cc_final: 0.8000 (m100) REVERT: 0 158 MET cc_start: 0.7504 (pmm) cc_final: 0.7092 (pmm) REVERT: 0 162 HIS cc_start: 0.7309 (m170) cc_final: 0.6864 (m170) REVERT: 0 254 PHE cc_start: 0.9589 (m-10) cc_final: 0.9382 (m-80) REVERT: 0 268 TYR cc_start: 0.8358 (t80) cc_final: 0.8146 (t80) REVERT: 2 145 VAL cc_start: 0.7079 (t) cc_final: 0.6765 (t) REVERT: 2 162 HIS cc_start: 0.7416 (m90) cc_final: 0.7152 (m-70) REVERT: 2 260 GLN cc_start: 0.6097 (mt0) cc_final: 0.5827 (mp10) REVERT: 4 201 MET cc_start: 0.1930 (pmm) cc_final: 0.1644 (ptm) outliers start: 1 outliers final: 1 residues processed: 591 average time/residue: 0.2929 time to fit residues: 271.7666 Evaluate side-chains 465 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 396 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN C 279 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN J 325 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 GLN N 193 GLN N 303 ASN N 325 GLN P 279 GLN P 325 GLN R 212 ASN R 279 GLN 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 325 GLN D 279 GLN D 325 GLN 0 279 GLN 0 303 ASN ** 0 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3969 r_free = 0.3969 target = 0.077458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.062827 restraints weight = 261781.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.064325 restraints weight = 195239.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.065524 restraints weight = 153820.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.066473 restraints weight = 125657.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.067192 restraints weight = 105881.473| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.9806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41757 Z= 0.152 Angle : 0.752 10.940 56592 Z= 0.377 Chirality : 0.048 0.286 6512 Planarity : 0.005 0.087 7120 Dihedral : 20.387 177.746 6816 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.02 % Allowed : 1.19 % Favored : 98.78 % 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 are not related in a simple way. whole: -0.24 (0.12), residues: 5216 helix: 0.55 (0.11), residues: 2272 sheet: 0.63 (0.19), residues: 784 loop : -1.18 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG W 242 TYR 0.103 0.005 TYR 0 102 PHE 0.034 0.001 PHE W 190 TRP 0.005 0.001 TRP D 289 HIS 0.005 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (41712) covalent geometry : angle 0.75174 / 0.38 (56592) hydrogen bonds : bond 0.03677 / 2.48 ( 1904) hydrogen bonds : angle 5.11478 / 3.78 ( 5472) Misc. bond : bond 0.00997 / 0.65 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9208.20 seconds wall clock time: 159 minutes 50.96 seconds (9590.96 seconds total)