Starting phenix.real_space_refine on Fri Mar 6 22:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oj5_12938/03_2026/7oj5_12938.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians Mn 48 7.51 5 S 72 5.16 5 C 21384 2.51 5 N 6336 2.21 5 O 7483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35323 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1431 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y Time building chain proxies: 3.14, per 1000 atoms: 0.09 Number of scatterers: 35323 At special positions: 0 Unit cell: (129.86, 129.86, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 48 24.99 S 72 16.00 O 7483 8.00 N 6336 7.00 C 21384 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=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 40.2% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN B 119 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 160 Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 160 Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 160 Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 Processing helix chain 'E' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN E 119 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 120 " --> pdb=" O MET E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 160 Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'F' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN F 119 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 160 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN G 119 " --> pdb=" O HIS G 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 160 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 256 Processing helix chain 'H' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN H 119 " --> pdb=" O HIS H 115 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 120 " --> pdb=" O MET H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 160 Processing helix chain 'H' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 256 Processing helix chain 'I' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 120 " --> pdb=" O MET I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 160 Processing helix chain 'I' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS I 213 " --> pdb=" O GLN I 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 256 Processing helix chain 'J' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN J 119 " --> pdb=" O HIS J 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 120 " --> pdb=" O MET J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 160 Processing helix chain 'J' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS J 213 " --> pdb=" O GLN J 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 256 Processing helix chain 'K' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN K 119 " --> pdb=" O HIS K 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 160 Processing helix chain 'K' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS K 213 " --> pdb=" O GLN K 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 256 Processing helix chain 'L' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN L 119 " --> pdb=" O HIS L 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L 120 " --> pdb=" O MET L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 160 Processing helix chain 'L' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS L 213 " --> pdb=" O GLN L 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 256 Processing helix chain 'M' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN M 119 " --> pdb=" O HIS M 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU M 120 " --> pdb=" O MET M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 160 Processing helix chain 'M' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS M 213 " --> pdb=" O GLN M 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 256 Processing helix chain 'N' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN N 119 " --> pdb=" O HIS N 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 120 " --> pdb=" O MET N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 160 Processing helix chain 'N' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS N 213 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 256 Processing helix chain 'O' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN O 119 " --> pdb=" O HIS O 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 120 " --> pdb=" O MET O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 160 Processing helix chain 'O' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS O 213 " --> pdb=" O GLN O 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR O 221 " --> pdb=" O SER O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 256 Processing helix chain 'P' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN P 119 " --> pdb=" O HIS P 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 120 " --> pdb=" O MET P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 160 Processing helix chain 'P' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS P 213 " --> pdb=" O GLN P 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR P 221 " --> pdb=" O SER P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 256 Processing helix chain 'Q' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN Q 119 " --> pdb=" O HIS Q 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Q 120 " --> pdb=" O MET Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 160 Processing helix chain 'Q' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS Q 213 " --> pdb=" O GLN Q 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Q 221 " --> pdb=" O SER Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 256 Processing helix chain 'R' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS R 213 " --> pdb=" O GLN R 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 256 Processing helix chain 'S' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN S 119 " --> pdb=" O HIS S 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU S 120 " --> pdb=" O MET S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 160 Processing helix chain 'S' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS S 213 " --> pdb=" O GLN S 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR S 221 " --> pdb=" O SER S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 256 Processing helix chain 'T' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN T 119 " --> pdb=" O HIS T 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 120 " --> pdb=" O MET T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 160 Processing helix chain 'T' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS T 213 " --> pdb=" O GLN T 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR T 221 " --> pdb=" O SER T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 256 Processing helix chain 'V' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN V 119 " --> pdb=" O HIS V 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU V 120 " --> pdb=" O MET V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 160 Processing helix chain 'V' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS V 213 " --> pdb=" O GLN V 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR V 221 " --> pdb=" O SER V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 256 Processing helix chain 'W' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN W 119 " --> pdb=" O HIS W 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU W 120 " --> pdb=" O MET W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 160 Processing helix chain 'W' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS W 213 " --> pdb=" O GLN W 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR W 221 " --> pdb=" O SER W 217 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 256 Processing helix chain 'X' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN X 119 " --> pdb=" O HIS X 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU X 120 " --> pdb=" O MET X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 160 Processing helix chain 'X' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS X 213 " --> pdb=" O GLN X 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR X 221 " --> pdb=" O SER X 217 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 256 Processing helix chain 'Y' and resid 110 through 125 removed outlier: 3.690A pdb=" N GLN Y 119 " --> pdb=" O HIS Y 115 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Y 120 " --> pdb=" O MET Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 160 Processing helix chain 'Y' and resid 209 through 223 removed outlier: 3.779A pdb=" N HIS Y 213 " --> pdb=" O GLN Y 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Y 221 " --> pdb=" O SER Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU A 179 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS A 191 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 228 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 230 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP A 195 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER A 232 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 86 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU B 179 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS B 191 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE B 228 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN B 230 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP B 195 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER B 232 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 86 Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU C 179 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS C 191 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE C 228 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN C 230 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 195 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER C 232 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 86 Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU D 179 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS D 191 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE D 228 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN D 230 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP D 195 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER D 232 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 80 through 86 Processing sheet with id=AB1, first strand: chain 'E' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU E 179 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS E 191 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE E 228 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN E 230 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP E 195 " --> pdb=" O GLN E 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER E 232 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 86 Processing sheet with id=AB3, first strand: chain 'F' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU F 179 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS F 191 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 228 " --> pdb=" O HIS F 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY F 193 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN F 230 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP F 195 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER F 232 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 86 Processing sheet with id=AB5, first strand: chain 'G' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU G 179 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS G 191 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE G 228 " --> pdb=" O HIS G 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY G 193 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN G 230 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP G 195 " --> pdb=" O GLN G 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER G 232 " --> pdb=" O ASP G 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 86 Processing sheet with id=AB7, first strand: chain 'H' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU H 179 " --> pdb=" O PHE H 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS H 191 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE H 228 " --> pdb=" O HIS H 191 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY H 193 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLN H 230 " --> pdb=" O GLY H 193 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP H 195 " --> pdb=" O GLN H 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER H 232 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 80 through 86 Processing sheet with id=AB9, first strand: chain 'I' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU I 179 " --> pdb=" O PHE I 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS I 191 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE I 228 " --> pdb=" O HIS I 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY I 193 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN I 230 " --> pdb=" O GLY I 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP I 195 " --> pdb=" O GLN I 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER I 232 " --> pdb=" O ASP I 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 80 through 86 Processing sheet with id=AC2, first strand: chain 'J' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU J 179 " --> pdb=" O PHE J 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS J 191 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE J 228 " --> pdb=" O HIS J 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY J 193 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN J 230 " --> pdb=" O GLY J 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP J 195 " --> pdb=" O GLN J 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER J 232 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 80 through 86 Processing sheet with id=AC4, first strand: chain 'K' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU K 179 " --> pdb=" O PHE K 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS K 191 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE K 228 " --> pdb=" O HIS K 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY K 193 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN K 230 " --> pdb=" O GLY K 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP K 195 " --> pdb=" O GLN K 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER K 232 " --> pdb=" O ASP K 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 80 through 86 Processing sheet with id=AC6, first strand: chain 'L' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU L 179 " --> pdb=" O PHE L 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS L 191 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE L 228 " --> pdb=" O HIS L 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY L 193 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN L 230 " --> pdb=" O GLY L 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP L 195 " --> pdb=" O GLN L 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER L 232 " --> pdb=" O ASP L 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 80 through 86 Processing sheet with id=AC8, first strand: chain 'M' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU M 179 " --> pdb=" O PHE M 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS M 191 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE M 228 " --> pdb=" O HIS M 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY M 193 " --> pdb=" O ILE M 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN M 230 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP M 195 " --> pdb=" O GLN M 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER M 232 " --> pdb=" O ASP M 195 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 80 through 86 Processing sheet with id=AD1, first strand: chain 'N' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU N 179 " --> pdb=" O PHE N 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS N 191 " --> pdb=" O LEU N 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE N 228 " --> pdb=" O HIS N 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY N 193 " --> pdb=" O ILE N 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN N 230 " --> pdb=" O GLY N 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP N 195 " --> pdb=" O GLN N 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER N 232 " --> pdb=" O ASP N 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 80 through 86 Processing sheet with id=AD3, first strand: chain 'O' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU O 179 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS O 191 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE O 228 " --> pdb=" O HIS O 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY O 193 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN O 230 " --> pdb=" O GLY O 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP O 195 " --> pdb=" O GLN O 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER O 232 " --> pdb=" O ASP O 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 80 through 86 Processing sheet with id=AD5, first strand: chain 'P' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU P 179 " --> pdb=" O PHE P 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS P 191 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE P 228 " --> pdb=" O HIS P 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY P 193 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN P 230 " --> pdb=" O GLY P 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP P 195 " --> pdb=" O GLN P 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER P 232 " --> pdb=" O ASP P 195 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 80 through 86 Processing sheet with id=AD7, first strand: chain 'Q' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU Q 179 " --> pdb=" O PHE Q 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS Q 191 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE Q 228 " --> pdb=" O HIS Q 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY Q 193 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN Q 230 " --> pdb=" O GLY Q 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP Q 195 " --> pdb=" O GLN Q 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER Q 232 " --> pdb=" O ASP Q 195 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 80 through 86 Processing sheet with id=AD9, first strand: chain 'R' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU R 179 " --> pdb=" O PHE R 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS R 191 " --> pdb=" O LEU R 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE R 228 " --> pdb=" O HIS R 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY R 193 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN R 230 " --> pdb=" O GLY R 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP R 195 " --> pdb=" O GLN R 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER R 232 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 80 through 86 Processing sheet with id=AE2, first strand: chain 'S' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU S 179 " --> pdb=" O PHE S 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS S 191 " --> pdb=" O LEU S 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE S 228 " --> pdb=" O HIS S 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY S 193 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN S 230 " --> pdb=" O GLY S 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP S 195 " --> pdb=" O GLN S 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER S 232 " --> pdb=" O ASP S 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 80 through 86 Processing sheet with id=AE4, first strand: chain 'T' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU T 179 " --> pdb=" O PHE T 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS T 191 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE T 228 " --> pdb=" O HIS T 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY T 193 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN T 230 " --> pdb=" O GLY T 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP T 195 " --> pdb=" O GLN T 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER T 232 " --> pdb=" O ASP T 195 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 80 through 86 Processing sheet with id=AE6, first strand: chain 'V' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU V 179 " --> pdb=" O PHE V 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS V 191 " --> pdb=" O LEU V 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE V 228 " --> pdb=" O HIS V 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY V 193 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN V 230 " --> pdb=" O GLY V 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP V 195 " --> pdb=" O GLN V 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER V 232 " --> pdb=" O ASP V 195 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 80 through 86 Processing sheet with id=AE8, first strand: chain 'W' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU W 179 " --> pdb=" O PHE W 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS W 191 " --> pdb=" O LEU W 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE W 228 " --> pdb=" O HIS W 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY W 193 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN W 230 " --> pdb=" O GLY W 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP W 195 " --> pdb=" O GLN W 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER W 232 " --> pdb=" O ASP W 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 80 through 86 Processing sheet with id=AF1, first strand: chain 'X' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU X 179 " --> pdb=" O PHE X 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS X 191 " --> pdb=" O LEU X 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE X 228 " --> pdb=" O HIS X 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY X 193 " --> pdb=" O ILE X 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN X 230 " --> pdb=" O GLY X 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP X 195 " --> pdb=" O GLN X 230 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER X 232 " --> pdb=" O ASP X 195 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 80 through 86 Processing sheet with id=AF3, first strand: chain 'Y' and resid 168 through 175 removed outlier: 6.433A pdb=" N LEU Y 179 " --> pdb=" O PHE Y 231 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS Y 191 " --> pdb=" O LEU Y 226 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE Y 228 " --> pdb=" O HIS Y 191 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN Y 230 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP Y 195 " --> pdb=" O GLN Y 230 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER Y 232 " --> pdb=" O ASP Y 195 " (cutoff:3.500A) 2088 hydrogen bonds defined for protein. 6120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12000 1.34 - 1.46: 7223 1.46 - 1.58: 15625 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 34992 Sorted by residual: bond pdb=" CB MET H 116 " pdb=" CG MET H 116 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.51e-01 bond pdb=" CB MET Y 116 " pdb=" CG MET Y 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET K 116 " pdb=" CG MET K 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET J 116 " pdb=" CG MET J 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB MET R 116 " pdb=" CG MET R 116 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 ... (remaining 34987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 46417 1.46 - 2.92: 696 2.92 - 4.38: 191 4.38 - 5.84: 24 5.84 - 7.31: 24 Bond angle restraints: 47352 Sorted by residual: angle pdb=" CA GLU K 241 " pdb=" CB GLU K 241 " pdb=" CG GLU K 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU J 241 " pdb=" CB GLU J 241 " pdb=" CG GLU J 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU I 241 " pdb=" CB GLU I 241 " pdb=" CG GLU I 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU C 241 " pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLU P 241 " pdb=" CB GLU P 241 " pdb=" CG GLU P 241 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 ... (remaining 47347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 18072 17.45 - 34.90: 1896 34.90 - 52.36: 504 52.36 - 69.81: 144 69.81 - 87.26: 72 Dihedral angle restraints: 20688 sinusoidal: 8112 harmonic: 12576 Sorted by residual: dihedral pdb=" CA GLY H 204 " pdb=" C GLY H 204 " pdb=" N LYS H 205 " pdb=" CA LYS H 205 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY L 204 " pdb=" C GLY L 204 " pdb=" N LYS L 205 " pdb=" CA LYS L 205 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY Y 204 " pdb=" C GLY Y 204 " pdb=" N LYS Y 205 " pdb=" CA LYS Y 205 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2805 0.025 - 0.050: 1612 0.050 - 0.074: 526 0.074 - 0.099: 121 0.099 - 0.124: 336 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA ILE H 228 " pdb=" N ILE H 228 " pdb=" C ILE H 228 " pdb=" CB ILE H 228 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ARG P 167 " pdb=" N ARG P 167 " pdb=" C ARG P 167 " pdb=" CB ARG P 167 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ARG C 167 " pdb=" N ARG C 167 " pdb=" C ARG C 167 " pdb=" CB ARG C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 5397 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE X 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO X 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO X 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 199 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE T 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO T 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO T 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO T 199 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 198 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO Q 199 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO Q 199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO Q 199 " -0.016 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1194 2.72 - 3.27: 32251 3.27 - 3.81: 57475 3.81 - 4.36: 77663 4.36 - 4.90: 125243 Nonbonded interactions: 293826 Sorted by model distance: nonbonded pdb=" OE1 GLU Q 241 " pdb="MN MN Q 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU X 241 " pdb="MN MN X 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU B 241 " pdb="MN MN B 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU N 241 " pdb="MN MN N 302 " model vdw 2.177 2.320 nonbonded pdb=" OE1 GLU T 241 " pdb="MN MN T 302 " model vdw 2.177 2.320 ... (remaining 293821 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 26.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 0.002 0.030 34992 Z= 0.100 Angle : 0.531 7.305 47352 Z= 0.282 Chirality : 0.043 0.124 5400 Planarity : 0.003 0.028 6240 Dihedral : 16.614 87.261 12576 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.95 % Allowed : 13.64 % Favored : 84.42 % 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: -0.94 (0.12), residues: 4368 helix: -0.83 (0.11), residues: 1656 sheet: 1.13 (0.14), residues: 1152 loop : -1.65 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 167 TYR 0.006 0.001 TYR H 206 PHE 0.005 0.001 PHE C 112 HIS 0.005 0.001 HIS H 237 Details of bonding type rmsd covalent geometry : bond 0.00199 (34992) covalent geometry : angle 0.53129 (47352) hydrogen bonds : bond 0.26324 ( 2088) hydrogen bonds : angle 7.24152 ( 6120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 648 time to evaluate : 1.313 Fit side-chains REVERT: A 229 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7872 (mtp85) REVERT: B 229 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7873 (mtp85) REVERT: C 229 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7878 (mtp85) REVERT: D 229 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7872 (mtp85) REVERT: E 229 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7869 (mtp85) REVERT: F 229 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7875 (mtp85) REVERT: G 229 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7869 (mtp85) REVERT: H 229 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7871 (mtp85) REVERT: I 229 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7874 (mtp85) REVERT: J 229 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7873 (mtp85) REVERT: K 229 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7877 (mtp85) REVERT: L 229 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7869 (mtp85) REVERT: M 229 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7877 (mtp85) REVERT: N 229 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7870 (mtp85) REVERT: O 229 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7871 (mtp85) REVERT: P 229 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7878 (mtp85) REVERT: Q 229 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7872 (mtp85) REVERT: R 229 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7867 (mtp85) REVERT: S 229 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7872 (mtp85) REVERT: T 229 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7871 (mtp85) REVERT: V 229 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7879 (mtp85) REVERT: W 229 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7871 (mtp85) REVERT: X 229 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7873 (mtp85) REVERT: Y 229 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7873 (mtp85) outliers start: 72 outliers final: 24 residues processed: 720 average time/residue: 0.8364 time to fit residues: 705.4594 Evaluate side-chains 672 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 648 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain Y residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 97 ASN A 115 HIS A 157 GLN A 201 GLN B 91 ASN B 97 ASN B 115 HIS B 157 GLN B 201 GLN C 91 ASN C 97 ASN C 115 HIS C 157 GLN C 201 GLN D 91 ASN D 97 ASN D 115 HIS D 157 GLN D 201 GLN E 91 ASN E 97 ASN E 115 HIS E 157 GLN E 201 GLN F 91 ASN F 97 ASN F 115 HIS F 157 GLN F 201 GLN G 91 ASN G 97 ASN G 115 HIS G 157 GLN G 201 GLN H 91 ASN H 97 ASN H 115 HIS H 157 GLN H 201 GLN I 91 ASN I 97 ASN I 115 HIS I 157 GLN I 201 GLN J 91 ASN J 97 ASN J 115 HIS J 157 GLN J 201 GLN K 91 ASN K 97 ASN K 115 HIS K 157 GLN K 201 GLN L 91 ASN L 97 ASN L 115 HIS L 157 GLN L 201 GLN M 91 ASN M 97 ASN M 115 HIS M 157 GLN M 201 GLN N 91 ASN N 97 ASN N 115 HIS N 157 GLN N 201 GLN O 91 ASN O 97 ASN O 115 HIS O 157 GLN O 201 GLN P 91 ASN P 97 ASN P 115 HIS P 157 GLN P 201 GLN Q 91 ASN Q 97 ASN Q 115 HIS Q 157 GLN Q 201 GLN R 91 ASN R 97 ASN R 115 HIS R 157 GLN R 201 GLN S 91 ASN S 97 ASN S 115 HIS S 157 GLN S 201 GLN T 91 ASN T 97 ASN T 115 HIS T 157 GLN T 201 GLN V 91 ASN V 97 ASN V 115 HIS V 157 GLN V 201 GLN W 91 ASN W 97 ASN W 115 HIS W 157 GLN W 201 GLN X 91 ASN X 97 ASN X 115 HIS X 157 GLN X 201 GLN Y 91 ASN Y 97 ASN Y 115 HIS Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.145520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.126714 restraints weight = 27604.029| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.71 r_work: 0.3160 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34992 Z= 0.218 Angle : 0.737 6.821 47352 Z= 0.406 Chirality : 0.049 0.158 5400 Planarity : 0.005 0.034 6240 Dihedral : 5.103 18.284 4752 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.95 % Allowed : 12.99 % Favored : 85.06 % 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: 0.55 (0.13), residues: 4368 helix: 1.67 (0.12), residues: 1656 sheet: 1.00 (0.14), residues: 1152 loop : -1.63 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 167 TYR 0.010 0.003 TYR O 194 PHE 0.014 0.003 PHE W 215 HIS 0.005 0.002 HIS H 237 Details of bonding type rmsd covalent geometry : bond 0.00416 (34992) covalent geometry : angle 0.73693 (47352) hydrogen bonds : bond 0.08821 ( 2088) hydrogen bonds : angle 4.68879 ( 6120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 648 time to evaluate : 1.365 Fit side-chains REVERT: A 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8606 (mtp85) REVERT: A 261 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.2429 (mtp85) REVERT: B 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8610 (mtp85) REVERT: B 261 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2437 (mtp85) REVERT: C 229 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8602 (mtp85) REVERT: C 261 ARG cc_start: 0.4907 (OUTLIER) cc_final: 0.2434 (mtp85) REVERT: D 229 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8607 (mtp85) REVERT: D 261 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.2432 (mtp85) REVERT: E 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8615 (mtp85) REVERT: E 261 ARG cc_start: 0.4924 (OUTLIER) cc_final: 0.2435 (mtp85) REVERT: F 229 ARG cc_start: 0.8830 (ttm170) cc_final: 0.8617 (mtp85) REVERT: F 261 ARG cc_start: 0.4907 (OUTLIER) cc_final: 0.2442 (mtp85) REVERT: G 229 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8614 (mtp85) REVERT: G 261 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.2433 (mtp85) REVERT: H 229 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8609 (mtp85) REVERT: H 261 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.2433 (mtp85) REVERT: I 229 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8610 (mtp85) REVERT: I 261 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.2434 (mtp85) REVERT: J 229 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8604 (mtp85) REVERT: J 261 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.2429 (mtp85) REVERT: K 229 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8612 (mtp85) REVERT: K 261 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.2432 (mtp85) REVERT: L 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8620 (mtp85) REVERT: L 261 ARG cc_start: 0.4907 (OUTLIER) cc_final: 0.2435 (mtp85) REVERT: M 229 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8603 (mtp85) REVERT: M 261 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.2433 (mtp85) REVERT: N 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8627 (mtp85) REVERT: N 261 ARG cc_start: 0.4903 (OUTLIER) cc_final: 0.2441 (mtp85) REVERT: O 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8609 (mtp85) REVERT: O 261 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.2422 (mtp85) REVERT: P 229 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8604 (mtp85) REVERT: P 261 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.2432 (mtp85) REVERT: Q 229 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8616 (mtp85) REVERT: Q 261 ARG cc_start: 0.4907 (OUTLIER) cc_final: 0.2438 (mtp85) REVERT: R 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8616 (mtp85) REVERT: R 261 ARG cc_start: 0.4909 (OUTLIER) cc_final: 0.2435 (mtp85) REVERT: S 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8608 (mtp85) REVERT: S 261 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.2431 (mtp85) REVERT: T 229 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8614 (mtp85) REVERT: T 261 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.2438 (mtp85) REVERT: V 229 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8607 (mtp85) REVERT: V 261 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.2436 (mtp85) REVERT: W 229 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8611 (mtp85) REVERT: W 261 ARG cc_start: 0.4908 (OUTLIER) cc_final: 0.2430 (mtp85) REVERT: X 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8617 (mtp85) REVERT: X 261 ARG cc_start: 0.4913 (OUTLIER) cc_final: 0.2441 (mtp85) REVERT: Y 229 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8606 (mtp85) REVERT: Y 261 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2434 (mtp85) outliers start: 72 outliers final: 24 residues processed: 696 average time/residue: 0.9278 time to fit residues: 743.6545 Evaluate side-chains 624 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 576 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 59 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 305 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 201 GLN B 91 ASN B 157 GLN B 201 GLN C 91 ASN C 157 GLN C 201 GLN D 91 ASN D 157 GLN D 201 GLN E 91 ASN E 157 GLN E 201 GLN F 91 ASN F 157 GLN F 201 GLN G 91 ASN G 157 GLN G 201 GLN H 91 ASN H 157 GLN H 201 GLN I 91 ASN I 157 GLN I 201 GLN J 91 ASN J 157 GLN J 201 GLN K 91 ASN K 157 GLN K 201 GLN L 91 ASN L 157 GLN L 201 GLN M 91 ASN M 157 GLN M 201 GLN N 91 ASN N 157 GLN N 201 GLN O 91 ASN O 157 GLN O 201 GLN P 91 ASN P 157 GLN P 201 GLN Q 91 ASN Q 157 GLN Q 201 GLN R 91 ASN R 157 GLN R 201 GLN S 91 ASN S 157 GLN S 201 GLN T 91 ASN T 157 GLN T 201 GLN V 91 ASN V 157 GLN V 201 GLN W 91 ASN W 157 GLN W 201 GLN X 91 ASN X 157 GLN X 201 GLN Y 91 ASN Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.124946 restraints weight = 27204.241| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.75 r_work: 0.3134 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 34992 Z= 0.296 Angle : 0.871 8.017 47352 Z= 0.474 Chirality : 0.056 0.251 5400 Planarity : 0.005 0.039 6240 Dihedral : 5.412 18.964 4728 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 12.34 % Favored : 85.71 % 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: 0.58 (0.13), residues: 4368 helix: 1.68 (0.11), residues: 1680 sheet: 0.41 (0.13), residues: 1344 loop : -1.27 (0.20), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 167 TYR 0.012 0.004 TYR F 194 PHE 0.018 0.004 PHE Q 215 HIS 0.008 0.002 HIS V 237 Details of bonding type rmsd covalent geometry : bond 0.00590 (34992) covalent geometry : angle 0.87103 (47352) hydrogen bonds : bond 0.09792 ( 2088) hydrogen bonds : angle 4.70765 ( 6120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 648 time to evaluate : 1.310 Fit side-chains REVERT: A 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8605 (mtp85) REVERT: A 261 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.2445 (mtm180) REVERT: B 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8614 (mtp85) REVERT: B 261 ARG cc_start: 0.4951 (OUTLIER) cc_final: 0.2449 (mtm180) REVERT: C 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8609 (mtp85) REVERT: C 261 ARG cc_start: 0.4933 (OUTLIER) cc_final: 0.2434 (mtm180) REVERT: D 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8602 (mtp85) REVERT: D 261 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.2446 (mtm180) REVERT: E 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8612 (mtp85) REVERT: E 261 ARG cc_start: 0.4964 (OUTLIER) cc_final: 0.2438 (mtm180) REVERT: F 229 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8615 (mtp85) REVERT: F 261 ARG cc_start: 0.4948 (OUTLIER) cc_final: 0.2447 (mtm180) REVERT: G 229 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8607 (mtp85) REVERT: G 261 ARG cc_start: 0.4951 (OUTLIER) cc_final: 0.2440 (mtm180) REVERT: H 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8600 (mtp85) REVERT: H 261 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.2440 (mtm180) REVERT: I 229 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8605 (mtp85) REVERT: I 261 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.2437 (mtm180) REVERT: J 229 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8601 (mtp85) REVERT: J 261 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.2436 (mtm180) REVERT: K 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8609 (mtp85) REVERT: K 261 ARG cc_start: 0.4955 (OUTLIER) cc_final: 0.2438 (mtm180) REVERT: L 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8614 (mtp85) REVERT: L 261 ARG cc_start: 0.4937 (OUTLIER) cc_final: 0.2445 (mtm180) REVERT: M 229 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8605 (mtp85) REVERT: M 261 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.2441 (mtm180) REVERT: N 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8610 (mtp85) REVERT: N 261 ARG cc_start: 0.4943 (OUTLIER) cc_final: 0.2445 (mtm180) REVERT: O 229 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8604 (mtp85) REVERT: O 261 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.2439 (mtm180) REVERT: P 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8607 (mtp85) REVERT: P 261 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.2438 (mtm180) REVERT: Q 229 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8611 (mtp85) REVERT: Q 261 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.2447 (mtm180) REVERT: R 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8610 (mtp85) REVERT: R 261 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.2441 (mtm180) REVERT: S 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8606 (mtp85) REVERT: S 261 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.2434 (mtm180) REVERT: T 229 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8610 (mtp85) REVERT: T 261 ARG cc_start: 0.4946 (OUTLIER) cc_final: 0.2446 (mtm180) REVERT: V 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8609 (mtp85) REVERT: V 261 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2442 (mtm180) REVERT: W 229 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8606 (mtp85) REVERT: W 261 ARG cc_start: 0.4959 (OUTLIER) cc_final: 0.2435 (mtm180) REVERT: X 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8614 (mtp85) REVERT: X 261 ARG cc_start: 0.4933 (OUTLIER) cc_final: 0.2445 (mtm180) REVERT: Y 229 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8608 (mtp85) REVERT: Y 261 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.2443 (mtm180) outliers start: 72 outliers final: 24 residues processed: 696 average time/residue: 0.9492 time to fit residues: 755.6114 Evaluate side-chains 648 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 600 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 76 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 425 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 170 ASN A 201 GLN B 91 ASN B 157 GLN B 170 ASN B 201 GLN C 91 ASN C 157 GLN C 170 ASN C 201 GLN D 91 ASN D 157 GLN D 170 ASN D 201 GLN E 91 ASN E 157 GLN E 170 ASN E 201 GLN F 91 ASN F 157 GLN F 170 ASN F 201 GLN G 91 ASN G 157 GLN G 170 ASN G 201 GLN H 91 ASN H 157 GLN H 170 ASN H 201 GLN I 91 ASN I 157 GLN I 170 ASN I 201 GLN J 91 ASN J 157 GLN J 170 ASN J 201 GLN K 91 ASN K 157 GLN K 170 ASN K 201 GLN L 91 ASN L 157 GLN L 170 ASN L 201 GLN M 91 ASN M 157 GLN M 170 ASN M 201 GLN N 91 ASN N 157 GLN N 170 ASN N 201 GLN O 91 ASN O 157 GLN O 170 ASN O 201 GLN P 91 ASN P 157 GLN P 170 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 170 ASN Q 201 GLN R 91 ASN R 157 GLN R 170 ASN R 201 GLN S 91 ASN S 157 GLN S 170 ASN S 201 GLN T 91 ASN T 157 GLN T 170 ASN T 201 GLN V 91 ASN V 157 GLN V 170 ASN V 201 GLN W 91 ASN W 157 GLN W 170 ASN W 201 GLN X 91 ASN X 157 GLN X 170 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 170 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.142676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.124668 restraints weight = 27055.413| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.76 r_work: 0.3132 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 34992 Z= 0.309 Angle : 0.889 8.136 47352 Z= 0.485 Chirality : 0.058 0.255 5400 Planarity : 0.005 0.040 6240 Dihedral : 5.485 19.246 4728 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 11.72 % Favored : 85.69 % 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: 0.43 (0.12), residues: 4368 helix: 1.71 (0.11), residues: 1656 sheet: 0.78 (0.13), residues: 1152 loop : -1.73 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 167 TYR 0.012 0.004 TYR X 194 PHE 0.018 0.004 PHE E 215 HIS 0.008 0.002 HIS M 237 Details of bonding type rmsd covalent geometry : bond 0.00620 (34992) covalent geometry : angle 0.88851 (47352) hydrogen bonds : bond 0.09795 ( 2088) hydrogen bonds : angle 4.67987 ( 6120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 579 time to evaluate : 1.491 Fit side-chains REVERT: A 229 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8598 (mtp85) REVERT: A 261 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: B 229 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8614 (mtp85) REVERT: B 261 ARG cc_start: 0.4991 (OUTLIER) cc_final: 0.2543 (mtm180) REVERT: C 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8604 (mtp85) REVERT: C 261 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: D 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8604 (mtp85) REVERT: D 261 ARG cc_start: 0.4978 (OUTLIER) cc_final: 0.2543 (mtm180) REVERT: E 229 ARG cc_start: 0.8860 (ttm170) cc_final: 0.8615 (mtp85) REVERT: E 261 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: F 229 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8615 (mtp85) REVERT: F 261 ARG cc_start: 0.4987 (OUTLIER) cc_final: 0.2545 (mtm180) REVERT: G 229 ARG cc_start: 0.8858 (ttm170) cc_final: 0.8614 (mtp85) REVERT: G 261 ARG cc_start: 0.4982 (OUTLIER) cc_final: 0.2536 (mtm180) REVERT: H 229 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8603 (mtp85) REVERT: H 261 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.2541 (mtm180) REVERT: I 229 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8611 (mtp85) REVERT: I 261 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.2531 (mtm180) REVERT: J 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8606 (mtp85) REVERT: J 261 ARG cc_start: 0.4981 (OUTLIER) cc_final: 0.2541 (mtm180) REVERT: K 229 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8610 (mtp85) REVERT: K 261 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.2545 (mtm180) REVERT: L 229 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8614 (mtp85) REVERT: L 261 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: M 229 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8607 (mtp85) REVERT: M 261 ARG cc_start: 0.4984 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: N 229 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8611 (mtp85) REVERT: N 261 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.2547 (mtm180) REVERT: O 229 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8607 (mtp85) REVERT: O 261 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: P 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8604 (mtp85) REVERT: P 261 ARG cc_start: 0.4981 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: Q 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8615 (mtp85) REVERT: Q 261 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: R 229 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8610 (mtp85) REVERT: R 261 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: S 229 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8595 (mtp85) REVERT: S 261 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.2526 (mtm180) REVERT: T 229 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8611 (mtp85) REVERT: T 261 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.2546 (mtm180) REVERT: V 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8605 (mtp85) REVERT: V 261 ARG cc_start: 0.4958 (OUTLIER) cc_final: 0.2539 (mtm180) REVERT: W 229 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8611 (mtp85) REVERT: W 261 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.2528 (mtm180) REVERT: X 229 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8615 (mtp85) REVERT: X 261 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.2535 (mtm180) REVERT: Y 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8609 (mtp85) REVERT: Y 261 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.2539 (mtm180) outliers start: 96 outliers final: 48 residues processed: 651 average time/residue: 1.0184 time to fit residues: 755.7895 Evaluate side-chains 649 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 577 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 219 VAL Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 219 VAL Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 219 VAL Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 219 VAL Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 219 VAL Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 11 optimal weight: 9.9990 chunk 403 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 422 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 201 GLN B 91 ASN B 157 GLN B 201 GLN C 91 ASN C 157 GLN C 201 GLN D 91 ASN D 157 GLN D 201 GLN E 91 ASN E 157 GLN E 201 GLN F 91 ASN F 157 GLN F 201 GLN G 91 ASN G 157 GLN G 201 GLN H 91 ASN H 157 GLN H 201 GLN I 91 ASN I 157 GLN I 201 GLN J 91 ASN J 157 GLN J 201 GLN K 91 ASN K 157 GLN K 201 GLN L 91 ASN L 157 GLN L 201 GLN M 91 ASN M 157 GLN M 201 GLN N 91 ASN N 157 GLN N 201 GLN O 91 ASN O 157 GLN O 201 GLN P 91 ASN P 157 GLN P 201 GLN Q 91 ASN Q 157 GLN Q 201 GLN R 91 ASN R 157 GLN R 201 GLN S 91 ASN S 157 GLN S 201 GLN T 91 ASN T 157 GLN T 201 GLN V 91 ASN V 157 GLN V 201 GLN W 91 ASN W 157 GLN W 201 GLN X 91 ASN X 157 GLN X 201 GLN Y 91 ASN Y 157 GLN Y 201 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.143237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.125240 restraints weight = 27167.492| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.77 r_work: 0.3144 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 34992 Z= 0.275 Angle : 0.828 7.318 47352 Z= 0.453 Chirality : 0.055 0.220 5400 Planarity : 0.005 0.040 6240 Dihedral : 5.409 18.997 4728 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 11.04 % Favored : 87.01 % 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: 0.45 (0.12), residues: 4368 helix: 1.84 (0.11), residues: 1656 sheet: 0.72 (0.13), residues: 1152 loop : -1.80 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 167 TYR 0.010 0.004 TYR F 194 PHE 0.017 0.004 PHE V 215 HIS 0.007 0.002 HIS R 237 Details of bonding type rmsd covalent geometry : bond 0.00541 (34992) covalent geometry : angle 0.82798 (47352) hydrogen bonds : bond 0.09245 ( 2088) hydrogen bonds : angle 4.63362 ( 6120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 608 time to evaluate : 1.405 Fit side-chains REVERT: A 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8601 (mtp85) REVERT: A 261 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.2522 (mtm180) REVERT: B 229 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8622 (mtp85) REVERT: B 261 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.2522 (mtm180) REVERT: C 229 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8608 (mtp85) REVERT: C 261 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.2519 (mtm180) REVERT: D 229 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8612 (mtp85) REVERT: D 261 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: E 229 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8619 (mtp85) REVERT: E 261 ARG cc_start: 0.4971 (OUTLIER) cc_final: 0.2519 (mtm180) REVERT: F 229 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8620 (mtp85) REVERT: F 261 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: G 229 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8619 (mtp85) REVERT: G 261 ARG cc_start: 0.4964 (OUTLIER) cc_final: 0.2521 (mtm180) REVERT: H 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8611 (mtp85) REVERT: H 261 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.2528 (mtm180) REVERT: I 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8611 (mtp85) REVERT: I 261 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.2522 (mtm180) REVERT: J 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8610 (mtp85) REVERT: J 261 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.2530 (mtm180) REVERT: K 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8617 (mtp85) REVERT: K 261 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: L 229 ARG cc_start: 0.8858 (ttm170) cc_final: 0.8623 (mtp85) REVERT: L 261 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.2525 (mtm180) REVERT: M 229 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8603 (mtp85) REVERT: M 261 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.2521 (mtm180) REVERT: N 229 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8619 (mtp85) REVERT: N 261 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: O 229 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8612 (mtp85) REVERT: O 261 ARG cc_start: 0.4976 (OUTLIER) cc_final: 0.2524 (mtm180) REVERT: P 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8609 (mtp85) REVERT: P 261 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: Q 229 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8612 (mtp85) REVERT: Q 261 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.2522 (mtm180) REVERT: R 229 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8616 (mtp85) REVERT: R 261 ARG cc_start: 0.4970 (OUTLIER) cc_final: 0.2521 (mtm180) REVERT: S 229 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8599 (mtp85) REVERT: S 261 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.2514 (mtm180) REVERT: T 229 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8616 (mtp85) REVERT: T 261 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.2530 (mtm180) REVERT: V 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8610 (mtp85) REVERT: V 261 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.2525 (mtm180) REVERT: W 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8613 (mtp85) REVERT: W 261 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.2515 (mtm180) REVERT: X 229 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8623 (mtp85) REVERT: X 261 ARG cc_start: 0.4955 (OUTLIER) cc_final: 0.2521 (mtm180) REVERT: Y 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8610 (mtp85) REVERT: Y 261 ARG cc_start: 0.4975 (OUTLIER) cc_final: 0.2524 (mtm180) outliers start: 72 outliers final: 24 residues processed: 656 average time/residue: 1.0509 time to fit residues: 782.9067 Evaluate side-chains 627 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 579 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 89 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.126815 restraints weight = 27166.613| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.74 r_work: 0.3164 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34992 Z= 0.222 Angle : 0.740 6.404 47352 Z= 0.406 Chirality : 0.052 0.171 5400 Planarity : 0.004 0.040 6240 Dihedral : 5.229 18.618 4728 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.22 % Allowed : 9.77 % Favored : 87.01 % 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: 0.56 (0.13), residues: 4368 helix: 2.01 (0.11), residues: 1656 sheet: 0.77 (0.13), residues: 1152 loop : -1.83 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 167 TYR 0.009 0.003 TYR N 206 PHE 0.014 0.003 PHE N 215 HIS 0.006 0.001 HIS T 237 Details of bonding type rmsd covalent geometry : bond 0.00427 (34992) covalent geometry : angle 0.73996 (47352) hydrogen bonds : bond 0.08239 ( 2088) hydrogen bonds : angle 4.51443 ( 6120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 624 time to evaluate : 1.216 Fit side-chains REVERT: A 139 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7363 (t70) REVERT: A 229 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8595 (mtp85) REVERT: A 261 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.2490 (mtm180) REVERT: B 139 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7358 (t70) REVERT: B 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8623 (mtp85) REVERT: B 261 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.2496 (mtm180) REVERT: C 139 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7364 (t70) REVERT: C 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8604 (mtp85) REVERT: C 261 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2497 (mtm180) REVERT: D 139 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7369 (t70) REVERT: D 229 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8607 (mtp85) REVERT: D 261 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.2503 (mtm180) REVERT: E 139 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7361 (t70) REVERT: E 229 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8618 (mtp85) REVERT: E 261 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.2484 (mtm180) REVERT: F 139 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7383 (t70) REVERT: F 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8621 (mtp85) REVERT: F 261 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.2504 (mtm180) REVERT: G 139 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7332 (t70) REVERT: G 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8619 (mtp85) REVERT: G 261 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.2494 (mtm180) REVERT: H 139 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7375 (t70) REVERT: H 229 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8610 (mtp85) REVERT: H 261 ARG cc_start: 0.4925 (OUTLIER) cc_final: 0.2500 (mtm180) REVERT: I 139 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: I 229 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8610 (mtp85) REVERT: I 261 ARG cc_start: 0.4936 (OUTLIER) cc_final: 0.2494 (mtm180) REVERT: J 139 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7379 (t70) REVERT: J 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8608 (mtp85) REVERT: J 261 ARG cc_start: 0.4923 (OUTLIER) cc_final: 0.2500 (mtm180) REVERT: K 139 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7362 (t70) REVERT: K 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8617 (mtp85) REVERT: K 261 ARG cc_start: 0.4925 (OUTLIER) cc_final: 0.2506 (mtm180) REVERT: L 139 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7324 (t70) REVERT: L 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8622 (mtp85) REVERT: L 261 ARG cc_start: 0.4910 (OUTLIER) cc_final: 0.2497 (mtm180) REVERT: M 139 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7345 (t70) REVERT: M 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8608 (mtp85) REVERT: M 261 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.2493 (mtm180) REVERT: N 139 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7378 (t70) REVERT: N 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8622 (mtp85) REVERT: N 261 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.2509 (mtm180) REVERT: O 139 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7357 (t70) REVERT: O 229 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8611 (mtp85) REVERT: O 261 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.2494 (mtm180) REVERT: P 139 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7363 (t70) REVERT: P 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8610 (mtp85) REVERT: P 261 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.2496 (mtm180) REVERT: Q 139 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: Q 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8613 (mtp85) REVERT: Q 261 ARG cc_start: 0.4925 (OUTLIER) cc_final: 0.2496 (mtm180) REVERT: R 139 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: R 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8612 (mtp85) REVERT: R 261 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.2493 (mtm180) REVERT: S 139 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: S 229 ARG cc_start: 0.8813 (ttm170) cc_final: 0.8596 (mtp85) REVERT: S 261 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.2478 (mtm180) REVERT: T 139 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7366 (t70) REVERT: T 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8616 (mtp85) REVERT: T 261 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.2501 (mtm180) REVERT: V 139 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: V 229 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8609 (mtp85) REVERT: V 261 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.2497 (mtm180) REVERT: W 139 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (t70) REVERT: W 229 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8604 (mtp85) REVERT: W 261 ARG cc_start: 0.4924 (OUTLIER) cc_final: 0.2487 (mtm180) REVERT: X 139 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7348 (t70) REVERT: X 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8627 (mtp85) REVERT: X 261 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.2492 (mtm180) REVERT: Y 139 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7346 (t70) REVERT: Y 229 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8607 (mtp85) REVERT: Y 261 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.2497 (mtm180) outliers start: 119 outliers final: 47 residues processed: 695 average time/residue: 0.8854 time to fit residues: 712.6193 Evaluate side-chains 719 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 624 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 259 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 259 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 139 ASP Chi-restraints excluded: chain T residue 259 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain V residue 259 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 259 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 139 ASP Chi-restraints excluded: chain Y residue 259 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 159 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 410 optimal weight: 3.9990 chunk 387 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.141982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123717 restraints weight = 26988.103| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.78 r_work: 0.3119 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 34992 Z= 0.342 Angle : 0.930 8.296 47352 Z= 0.508 Chirality : 0.061 0.288 5400 Planarity : 0.006 0.042 6240 Dihedral : 5.620 19.364 4728 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.14 % Allowed : 9.96 % Favored : 86.90 % 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: 0.37 (0.13), residues: 4368 helix: 1.60 (0.11), residues: 1680 sheet: 0.17 (0.13), residues: 1344 loop : -1.37 (0.20), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 167 TYR 0.014 0.005 TYR V 194 PHE 0.019 0.005 PHE N 215 HIS 0.009 0.002 HIS Y 237 Details of bonding type rmsd covalent geometry : bond 0.00695 (34992) covalent geometry : angle 0.93002 (47352) hydrogen bonds : bond 0.10329 ( 2088) hydrogen bonds : angle 4.73102 ( 6120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 624 time to evaluate : 1.438 Fit side-chains REVERT: A 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8598 (mtp85) REVERT: A 261 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.2530 (mtm180) REVERT: B 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8608 (mtp85) REVERT: B 261 ARG cc_start: 0.5019 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: C 229 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8599 (mtp85) REVERT: C 261 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.2531 (mtm180) REVERT: D 229 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8603 (mtp85) REVERT: D 261 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.2539 (mtm180) REVERT: E 229 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8616 (mtp85) REVERT: E 261 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.2524 (mtm180) REVERT: F 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8606 (mtp85) REVERT: F 261 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.2543 (mtm180) REVERT: G 229 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8617 (mtp85) REVERT: G 261 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.2526 (mtm180) REVERT: H 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8601 (mtp85) REVERT: H 261 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.2536 (mtm180) REVERT: I 229 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8601 (mtp85) REVERT: I 261 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.2520 (mtm180) REVERT: J 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8608 (mtp85) REVERT: J 261 ARG cc_start: 0.5028 (OUTLIER) cc_final: 0.2539 (mtm180) REVERT: K 229 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8610 (mtp85) REVERT: K 261 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: L 229 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8615 (mtp85) REVERT: L 261 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: M 229 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8595 (mtp85) REVERT: M 261 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.2529 (mtm180) REVERT: N 229 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8606 (mtp85) REVERT: N 261 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.2543 (mtm180) REVERT: O 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8609 (mtp85) REVERT: O 261 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.2536 (mtm180) REVERT: P 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8608 (mtp85) REVERT: P 261 ARG cc_start: 0.5019 (OUTLIER) cc_final: 0.2524 (mtm180) REVERT: Q 229 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8605 (mtp85) REVERT: Q 261 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: R 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8605 (mtp85) REVERT: R 261 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.2530 (mtm180) REVERT: S 229 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8597 (mtp85) REVERT: S 261 ARG cc_start: 0.5025 (OUTLIER) cc_final: 0.2523 (mtm180) REVERT: T 229 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8609 (mtp85) REVERT: T 261 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: V 229 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8597 (mtp85) REVERT: V 261 ARG cc_start: 0.5010 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: W 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8606 (mtp85) REVERT: W 261 ARG cc_start: 0.5025 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: X 229 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8615 (mtp85) REVERT: X 261 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.2534 (mtm180) REVERT: Y 229 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8602 (mtp85) REVERT: Y 261 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.2533 (mtm180) outliers start: 116 outliers final: 48 residues processed: 696 average time/residue: 0.9593 time to fit residues: 765.7292 Evaluate side-chains 696 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 624 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 259 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 259 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 259 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 259 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 259 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 259 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 182 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 426 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125264 restraints weight = 27084.944| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.75 r_work: 0.3141 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 34992 Z= 0.275 Angle : 0.830 7.144 47352 Z= 0.455 Chirality : 0.056 0.217 5400 Planarity : 0.005 0.040 6240 Dihedral : 5.453 19.222 4728 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 9.85 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4368 helix: 1.84 (0.11), residues: 1656 sheet: 0.71 (0.14), residues: 1152 loop : -1.72 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 167 TYR 0.012 0.004 TYR J 194 PHE 0.017 0.004 PHE V 215 HIS 0.008 0.002 HIS Y 237 Details of bonding type rmsd covalent geometry : bond 0.00543 (34992) covalent geometry : angle 0.83035 (47352) hydrogen bonds : bond 0.09148 ( 2088) hydrogen bonds : angle 4.60963 ( 6120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 648 time to evaluate : 1.257 Fit side-chains REVERT: A 229 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8595 (mtp85) REVERT: A 261 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: B 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8616 (mtp85) REVERT: B 261 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: C 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8603 (mtp85) REVERT: C 261 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.2535 (mtm180) REVERT: D 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8602 (mtp85) REVERT: D 261 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.2546 (mtm180) REVERT: E 229 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8618 (mtp85) REVERT: E 261 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: F 229 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8611 (mtp85) REVERT: F 261 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.2556 (mtm180) REVERT: G 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8620 (mtp85) REVERT: G 261 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.2541 (mtm180) REVERT: H 229 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8606 (mtp85) REVERT: H 261 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.2544 (mtm180) REVERT: I 229 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8602 (mtp85) REVERT: I 261 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.2538 (mtm180) REVERT: J 229 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8606 (mtp85) REVERT: J 261 ARG cc_start: 0.5044 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: K 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8612 (mtp85) REVERT: K 261 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.2549 (mtm180) REVERT: L 229 ARG cc_start: 0.8850 (ttm170) cc_final: 0.8617 (mtp85) REVERT: L 261 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.2544 (mtm180) REVERT: M 229 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8600 (mtp85) REVERT: M 261 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: N 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8608 (mtp85) REVERT: N 261 ARG cc_start: 0.5048 (OUTLIER) cc_final: 0.2555 (mtm180) REVERT: O 229 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8609 (mtp85) REVERT: O 261 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.2537 (mtm180) REVERT: P 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8604 (mtp85) REVERT: P 261 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.2541 (mtm180) REVERT: Q 229 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8602 (mtp85) REVERT: Q 261 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: R 229 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8603 (mtp85) REVERT: R 261 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.2541 (mtm180) REVERT: S 229 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8588 (mtp85) REVERT: S 261 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.2530 (mtm180) REVERT: T 229 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8611 (mtp85) REVERT: T 261 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.2539 (mtm180) REVERT: V 229 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8603 (mtp85) REVERT: V 261 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.2542 (mtm180) REVERT: W 229 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8602 (mtp85) REVERT: W 261 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.2531 (mtm180) REVERT: X 229 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8618 (mtp85) REVERT: X 261 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.2543 (mtm180) REVERT: Y 229 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8601 (mtp85) REVERT: Y 261 ARG cc_start: 0.5058 (OUTLIER) cc_final: 0.2548 (mtm180) outliers start: 96 outliers final: 48 residues processed: 720 average time/residue: 0.9133 time to fit residues: 758.0925 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 648 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 259 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 259 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 259 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 259 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 259 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 259 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 298 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 347 optimal weight: 2.9990 chunk 417 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 334 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.124321 restraints weight = 27034.544| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.73 r_work: 0.3137 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 34992 Z= 0.236 Angle : 0.772 6.824 47352 Z= 0.423 Chirality : 0.053 0.184 5400 Planarity : 0.005 0.039 6240 Dihedral : 5.324 18.740 4728 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.25 % Allowed : 9.20 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4368 helix: 1.93 (0.11), residues: 1656 sheet: 0.75 (0.14), residues: 1152 loop : -1.81 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 167 TYR 0.010 0.003 TYR T 194 PHE 0.015 0.003 PHE L 215 HIS 0.007 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00457 (34992) covalent geometry : angle 0.77172 (47352) hydrogen bonds : bond 0.08557 ( 2088) hydrogen bonds : angle 4.55103 ( 6120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 672 time to evaluate : 1.464 Fit side-chains REVERT: A 139 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: A 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8621 (mtp85) REVERT: A 261 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.2502 (mtm180) REVERT: B 139 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: B 229 ARG cc_start: 0.8872 (ttm170) cc_final: 0.8641 (mtp85) REVERT: B 261 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.2517 (mtm180) REVERT: C 139 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: C 229 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8628 (mtp85) REVERT: C 261 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.2512 (mtm180) REVERT: D 139 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: D 229 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8626 (mtp85) REVERT: D 261 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.2523 (mtm180) REVERT: E 139 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: E 229 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8641 (mtp85) REVERT: E 261 ARG cc_start: 0.5063 (OUTLIER) cc_final: 0.2512 (mtm180) REVERT: F 139 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: F 229 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8636 (mtp85) REVERT: F 261 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.2528 (mtm180) REVERT: G 139 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: G 229 ARG cc_start: 0.8875 (ttm170) cc_final: 0.8644 (mtp85) REVERT: G 261 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.2516 (mtm180) REVERT: H 139 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: H 229 ARG cc_start: 0.8864 (ttm170) cc_final: 0.8631 (mtp85) REVERT: H 261 ARG cc_start: 0.5048 (OUTLIER) cc_final: 0.2516 (mtm180) REVERT: I 139 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: I 229 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8625 (mtp85) REVERT: I 261 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.2516 (mtm180) REVERT: J 139 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: J 229 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8633 (mtp85) REVERT: J 261 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.2515 (mtm180) REVERT: K 139 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: K 229 ARG cc_start: 0.8860 (ttm170) cc_final: 0.8634 (mtp85) REVERT: K 261 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.2523 (mtm180) REVERT: L 139 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: L 229 ARG cc_start: 0.8874 (ttm170) cc_final: 0.8642 (mtp85) REVERT: L 261 ARG cc_start: 0.5042 (OUTLIER) cc_final: 0.2517 (mtm180) REVERT: M 139 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: M 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8624 (mtp85) REVERT: M 261 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.2519 (mtm180) REVERT: N 139 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: N 229 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8638 (mtp85) REVERT: N 261 ARG cc_start: 0.5055 (OUTLIER) cc_final: 0.2525 (mtm180) REVERT: O 139 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: O 229 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8633 (mtp85) REVERT: O 261 ARG cc_start: 0.5058 (OUTLIER) cc_final: 0.2517 (mtm180) REVERT: P 139 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: P 229 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8626 (mtp85) REVERT: P 261 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.2513 (mtm180) REVERT: Q 139 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: Q 229 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8629 (mtp85) REVERT: Q 261 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.2520 (mtm180) REVERT: R 139 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: R 229 ARG cc_start: 0.8860 (ttm170) cc_final: 0.8627 (mtp85) REVERT: R 261 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.2518 (mtm180) REVERT: S 139 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: S 229 ARG cc_start: 0.8843 (ttm170) cc_final: 0.8618 (mtp85) REVERT: S 261 ARG cc_start: 0.5059 (OUTLIER) cc_final: 0.2503 (mtm180) REVERT: T 139 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: T 229 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8638 (mtp85) REVERT: T 261 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.2515 (mtm180) REVERT: V 139 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: V 229 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8630 (mtp85) REVERT: V 261 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.2520 (mtm180) REVERT: W 139 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: W 229 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8627 (mtp85) REVERT: W 261 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.2506 (mtm180) REVERT: X 139 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: X 229 ARG cc_start: 0.8871 (ttm170) cc_final: 0.8642 (mtp85) REVERT: X 261 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.2520 (mtm180) REVERT: Y 139 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: Y 229 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8625 (mtp85) REVERT: Y 261 ARG cc_start: 0.5069 (OUTLIER) cc_final: 0.2522 (mtm180) outliers start: 120 outliers final: 48 residues processed: 744 average time/residue: 0.9230 time to fit residues: 791.1413 Evaluate side-chains 768 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 672 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 259 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 259 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 139 ASP Chi-restraints excluded: chain T residue 259 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain V residue 259 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 259 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 139 ASP Chi-restraints excluded: chain Y residue 259 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 406 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 170 ASN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 170 ASN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 170 ASN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 170 ASN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 170 ASN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 170 ASN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 170 ASN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 170 ASN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 170 ASN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 170 ASN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 170 ASN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 170 ASN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 170 ASN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 170 ASN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 170 ASN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 170 ASN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 170 ASN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 170 ASN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 170 ASN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 170 ASN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 170 ASN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 170 ASN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 170 ASN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 170 ASN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.126209 restraints weight = 27268.101| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.78 r_work: 0.3152 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34992 Z= 0.233 Angle : 0.773 6.855 47352 Z= 0.422 Chirality : 0.053 0.182 5400 Planarity : 0.005 0.039 6240 Dihedral : 5.309 18.583 4728 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.25 % Allowed : 9.20 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.13), residues: 4368 helix: 1.96 (0.11), residues: 1656 sheet: 0.74 (0.14), residues: 1152 loop : -1.81 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 167 TYR 0.010 0.003 TYR F 206 PHE 0.015 0.003 PHE X 215 HIS 0.007 0.001 HIS N 237 Details of bonding type rmsd covalent geometry : bond 0.00451 (34992) covalent geometry : angle 0.77262 (47352) hydrogen bonds : bond 0.08483 ( 2088) hydrogen bonds : angle 4.51341 ( 6120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 624 time to evaluate : 1.415 Fit side-chains REVERT: A 139 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: A 229 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8589 (mtp85) REVERT: A 261 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.2519 (mtm180) REVERT: B 139 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 229 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8594 (mtp85) REVERT: B 261 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.2525 (mtm180) REVERT: C 139 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: C 229 ARG cc_start: 0.8817 (ttm170) cc_final: 0.8593 (mtp85) REVERT: C 261 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.2522 (mtm180) REVERT: D 139 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: D 229 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8596 (mtp85) REVERT: D 261 ARG cc_start: 0.5073 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: E 139 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: E 229 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8613 (mtp85) REVERT: E 261 ARG cc_start: 0.5068 (OUTLIER) cc_final: 0.2514 (mtm180) REVERT: F 139 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: F 229 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8602 (mtp85) REVERT: F 261 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.2535 (mtm180) REVERT: G 139 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: G 229 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8613 (mtp85) REVERT: G 261 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.2521 (mtm180) REVERT: H 139 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: H 229 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8595 (mtp85) REVERT: H 261 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.2531 (mtm180) REVERT: I 139 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: I 229 ARG cc_start: 0.8807 (ttm170) cc_final: 0.8588 (mtp85) REVERT: I 261 ARG cc_start: 0.5069 (OUTLIER) cc_final: 0.2516 (mtm180) REVERT: J 139 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: J 229 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8598 (mtp85) REVERT: J 261 ARG cc_start: 0.5066 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: K 139 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: K 229 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8604 (mtp85) REVERT: K 261 ARG cc_start: 0.5059 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: L 139 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: L 229 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8606 (mtp85) REVERT: L 261 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.2531 (mtm180) REVERT: M 139 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: M 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8597 (mtp85) REVERT: M 261 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: N 139 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: N 229 ARG cc_start: 0.8817 (ttm170) cc_final: 0.8596 (mtp85) REVERT: N 261 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.2535 (mtm180) REVERT: O 139 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: O 229 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8602 (mtp85) REVERT: O 261 ARG cc_start: 0.5073 (OUTLIER) cc_final: 0.2524 (mtm180) REVERT: P 139 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: P 229 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8597 (mtp85) REVERT: P 261 ARG cc_start: 0.5058 (OUTLIER) cc_final: 0.2520 (mtm180) REVERT: Q 139 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: Q 229 ARG cc_start: 0.8815 (ttm170) cc_final: 0.8596 (mtp85) REVERT: Q 261 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.2527 (mtm180) REVERT: R 139 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: R 229 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8602 (mtp85) REVERT: R 261 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.2529 (mtm180) REVERT: S 139 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: S 229 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8593 (mtp85) REVERT: S 261 ARG cc_start: 0.5066 (OUTLIER) cc_final: 0.2517 (mtm180) REVERT: T 139 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: T 229 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8598 (mtp85) REVERT: T 261 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.2523 (mtm180) REVERT: V 139 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: V 229 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8600 (mtp85) REVERT: V 261 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.2533 (mtm180) REVERT: W 139 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: W 229 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8599 (mtp85) REVERT: W 261 ARG cc_start: 0.5059 (OUTLIER) cc_final: 0.2519 (mtm180) REVERT: X 139 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: X 229 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8610 (mtp85) REVERT: X 261 ARG cc_start: 0.5036 (OUTLIER) cc_final: 0.2532 (mtm180) REVERT: Y 139 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: Y 229 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8603 (mtp85) REVERT: Y 261 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.2528 (mtm180) outliers start: 120 outliers final: 48 residues processed: 696 average time/residue: 0.9049 time to fit residues: 729.0608 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 624 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 261 ARG Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 261 ARG Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 261 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 259 THR Chi-restraints excluded: chain K residue 261 ARG Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 259 THR Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 261 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 261 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 261 ARG Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 139 ASP Chi-restraints excluded: chain Q residue 259 THR Chi-restraints excluded: chain Q residue 261 ARG Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 261 ARG Chi-restraints excluded: chain S residue 133 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 259 THR Chi-restraints excluded: chain S residue 261 ARG Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 139 ASP Chi-restraints excluded: chain T residue 259 THR Chi-restraints excluded: chain T residue 261 ARG Chi-restraints excluded: chain V residue 133 THR Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain V residue 259 THR Chi-restraints excluded: chain V residue 261 ARG Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 259 THR Chi-restraints excluded: chain W residue 261 ARG Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 259 THR Chi-restraints excluded: chain X residue 261 ARG Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 139 ASP Chi-restraints excluded: chain Y residue 259 THR Chi-restraints excluded: chain Y residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 223 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 157 GLN A 197 ASN A 201 GLN B 91 ASN B 157 GLN B 197 ASN B 201 GLN C 91 ASN C 157 GLN C 197 ASN C 201 GLN D 91 ASN D 157 GLN D 197 ASN D 201 GLN E 91 ASN E 157 GLN E 197 ASN E 201 GLN F 91 ASN F 157 GLN F 197 ASN F 201 GLN G 91 ASN G 157 GLN G 197 ASN G 201 GLN H 91 ASN H 157 GLN H 197 ASN H 201 GLN I 91 ASN I 157 GLN I 197 ASN I 201 GLN J 91 ASN J 157 GLN J 197 ASN J 201 GLN K 91 ASN K 157 GLN K 197 ASN K 201 GLN L 91 ASN L 157 GLN L 197 ASN L 201 GLN M 91 ASN M 157 GLN M 197 ASN M 201 GLN N 91 ASN N 157 GLN N 197 ASN N 201 GLN O 91 ASN O 157 GLN O 197 ASN O 201 GLN P 91 ASN P 157 GLN P 197 ASN P 201 GLN Q 91 ASN Q 157 GLN Q 197 ASN Q 201 GLN R 91 ASN R 157 GLN R 197 ASN R 201 GLN S 91 ASN S 157 GLN S 197 ASN S 201 GLN T 91 ASN T 157 GLN T 197 ASN T 201 GLN V 91 ASN V 157 GLN V 197 ASN V 201 GLN W 91 ASN W 157 GLN W 197 ASN W 201 GLN X 91 ASN X 157 GLN X 197 ASN X 201 GLN Y 91 ASN Y 157 GLN Y 197 ASN Y 201 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.126332 restraints weight = 27111.939| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 0.66 r_work: 0.3166 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34992 Z= 0.237 Angle : 0.782 6.994 47352 Z= 0.426 Chirality : 0.053 0.189 5400 Planarity : 0.005 0.040 6240 Dihedral : 5.319 18.595 4728 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.25 % Allowed : 8.98 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 4368 helix: 1.95 (0.11), residues: 1656 sheet: 0.78 (0.14), residues: 1152 loop : -1.80 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 167 TYR 0.010 0.003 TYR G 194 PHE 0.015 0.003 PHE G 215 HIS 0.007 0.001 HIS J 237 Details of bonding type rmsd covalent geometry : bond 0.00462 (34992) covalent geometry : angle 0.78207 (47352) hydrogen bonds : bond 0.08542 ( 2088) hydrogen bonds : angle 4.53064 ( 6120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14596.49 seconds wall clock time: 248 minutes 16.03 seconds (14896.03 seconds total)