Starting phenix.real_space_refine on Wed Aug 27 01:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9i_5623/08_2025/3j9i_5623.map" } resolution = 3.3 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= -0.008 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29288 2.51 5 N 7840 2.21 5 O 8904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 280 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46228 Number of models: 1 Model: "" Number of chains: 2 Chain: "S" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1744 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Restraints were copied for chains: F, T, G, U, A, O, B, P, C, Q, D, R, E, M, 1, N, 2, H, V, I, W, J, X, K, Y, L Time building chain proxies: 4.77, per 1000 atoms: 0.10 Number of scatterers: 46228 At special positions: 0 Unit cell: (128.854, 130.069, 166.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8904 8.00 N 7840 7.00 C 29288 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: 3.95 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.2 microseconds 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11004 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 56 sheets defined 43.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'S' and resid 21 through 33 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER S 200 " --> pdb=" O ALA S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS S 230 " --> pdb=" O GLN S 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE S 232 " --> pdb=" O GLU S 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE Z 192 " --> pdb=" O PRO Z 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.638A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE M 192 " --> pdb=" O PRO M 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 33 Processing helix chain 'T' and resid 60 through 64 Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL T 116 " --> pdb=" O LEU T 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER T 200 " --> pdb=" O ALA T 196 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE T 232 " --> pdb=" O GLU T 228 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 166 Processing helix chain '1' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE 1 192 " --> pdb=" O PRO 1 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE N 192 " --> pdb=" O PRO N 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 33 Processing helix chain 'U' and resid 60 through 64 Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 Processing helix chain 'U' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS U 230 " --> pdb=" O GLN U 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE U 232 " --> pdb=" O GLU U 228 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 166 Processing helix chain '2' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE 2 192 " --> pdb=" O PRO 2 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE H 192 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 33 Processing helix chain 'O' and resid 60 through 64 Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 116 " --> pdb=" O LEU O 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER O 200 " --> pdb=" O ALA O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS O 230 " --> pdb=" O GLN O 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE V 192 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'P' and resid 60 through 64 Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL P 116 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'P' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER P 200 " --> pdb=" O ALA P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE W 192 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 3.636A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE J 192 " --> pdb=" O PRO J 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 33 Processing helix chain 'Q' and resid 60 through 64 Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER Q 200 " --> pdb=" O ALA Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS Q 230 " --> pdb=" O GLN Q 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE Q 232 " --> pdb=" O GLU Q 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE X 192 " --> pdb=" O PRO X 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.630A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.683A pdb=" N LYS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 removed outlier: 3.503A pdb=" N ILE K 192 " --> pdb=" O PRO K 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 33 Processing helix chain 'R' and resid 60 through 64 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.766A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE Y 192 " --> pdb=" O PRO Y 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.631A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 202 removed outlier: 3.877A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.684A pdb=" N LYS E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.767A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 3.637A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 removed outlier: 3.502A pdb=" N ILE L 192 " --> pdb=" O PRO L 188 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'S' and resid 162 through 165 Processing sheet with id=B, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'Z' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR Z 127 " --> pdb=" O THR Z 3 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL Z 120 " --> pdb=" O SER Z 112 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=F, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'M' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR M 127 " --> pdb=" O THR M 3 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL M 120 " --> pdb=" O SER M 112 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=J, first strand: chain 'T' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL T 74 " --> pdb=" O ILE T 70 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain '1' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR 1 127 " --> pdb=" O THR 1 3 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain '1' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL 1 120 " --> pdb=" O SER 1 112 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=N, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'N' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR N 127 " --> pdb=" O THR N 3 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL N 120 " --> pdb=" O SER N 112 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=R, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL U 74 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain '2' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR 2 127 " --> pdb=" O THR 2 3 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain '2' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=V, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR H 127 " --> pdb=" O THR H 3 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 120 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'O' and resid 162 through 165 Processing sheet with id=Z, first strand: chain 'O' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL O 74 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'V' and resid 124 through 128 removed outlier: 3.519A pdb=" N THR V 127 " --> pdb=" O THR V 3 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AD, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR I 127 " --> pdb=" O THR I 3 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL I 120 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'P' and resid 162 through 165 Processing sheet with id=AH, first strand: chain 'P' and resid 67 through 71 removed outlier: 6.541A pdb=" N VAL P 74 " --> pdb=" O ILE P 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'W' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR W 127 " --> pdb=" O THR W 3 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL W 120 " --> pdb=" O SER W 112 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AL, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR J 127 " --> pdb=" O THR J 3 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 120 " --> pdb=" O SER J 112 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AP, first strand: chain 'Q' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL Q 74 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'X' and resid 124 through 128 removed outlier: 3.517A pdb=" N THR X 127 " --> pdb=" O THR X 3 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.445A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL X 120 " --> pdb=" O SER X 112 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AT, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AU, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR K 127 " --> pdb=" O THR K 3 " (cutoff:3.500A) Processing sheet with id=AV, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 120 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing sheet with id=AW, first strand: chain 'R' and resid 162 through 165 Processing sheet with id=AX, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AY, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR Y 127 " --> pdb=" O THR Y 3 " (cutoff:3.500A) Processing sheet with id=AZ, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'E' and resid 162 through 165 Processing sheet with id=BB, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.542A pdb=" N VAL E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'L' and resid 124 through 128 removed outlier: 3.518A pdb=" N THR L 127 " --> pdb=" O THR L 3 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.444A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 120 " --> pdb=" O SER L 112 " (cutoff:3.500A) 2733 hydrogen bonds defined for protein. 7821 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: 12.88 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 8219 1.31 - 1.45: 14535 1.45 - 1.59: 22567 1.59 - 1.73: 1131 1.73 - 1.86: 364 Bond restraints: 46816 Sorted by residual: bond pdb=" CA PHE 2 111 " pdb=" C PHE 2 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.51e+02 bond pdb=" CA PHE M 111 " pdb=" C PHE M 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.51e+02 bond pdb=" CA PHE L 111 " pdb=" C PHE L 111 " ideal model delta sigma weight residual 1.522 1.375 0.147 1.20e-02 6.94e+03 1.50e+02 bond pdb=" CA PHE N 111 " pdb=" C PHE N 111 " ideal model delta sigma weight residual 1.522 1.376 0.147 1.20e-02 6.94e+03 1.50e+02 bond pdb=" CA PHE X 111 " pdb=" C PHE X 111 " ideal model delta sigma weight residual 1.522 1.376 0.147 1.20e-02 6.94e+03 1.50e+02 ... (remaining 46811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 39294 3.12 - 6.23: 18484 6.23 - 9.35: 4674 9.35 - 12.47: 674 12.47 - 15.59: 56 Bond angle restraints: 63182 Sorted by residual: angle pdb=" CA ASN N 24 " pdb=" C ASN N 24 " pdb=" N PHE N 25 " ideal model delta sigma weight residual 118.82 131.20 -12.38 1.26e+00 6.30e-01 9.65e+01 angle pdb=" CA ASN 1 24 " pdb=" C ASN 1 24 " pdb=" N PHE 1 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.63e+01 angle pdb=" CA ASN J 24 " pdb=" C ASN J 24 " pdb=" N PHE J 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.63e+01 angle pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " ideal model delta sigma weight residual 118.82 131.18 -12.36 1.26e+00 6.30e-01 9.62e+01 angle pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N PHE Y 25 " ideal model delta sigma weight residual 118.82 131.17 -12.35 1.26e+00 6.30e-01 9.61e+01 ... (remaining 63177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.48: 27020 25.48 - 50.96: 1071 50.96 - 76.44: 481 76.44 - 101.91: 100 101.91 - 127.39: 14 Dihedral angle restraints: 28686 sinusoidal: 11466 harmonic: 17220 Sorted by residual: dihedral pdb=" CA ASN N 24 " pdb=" C ASN N 24 " pdb=" N PHE N 25 " pdb=" CA PHE N 25 " ideal model delta harmonic sigma weight residual 180.00 52.61 127.39 0 5.00e+00 4.00e-02 6.49e+02 dihedral pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " pdb=" CA PHE W 25 " ideal model delta harmonic sigma weight residual 180.00 52.65 127.35 0 5.00e+00 4.00e-02 6.49e+02 dihedral pdb=" CA ASN H 24 " pdb=" C ASN H 24 " pdb=" N PHE H 25 " pdb=" CA PHE H 25 " ideal model delta harmonic sigma weight residual 180.00 52.66 127.34 0 5.00e+00 4.00e-02 6.49e+02 ... (remaining 28683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 4706 0.205 - 0.411: 2126 0.411 - 0.616: 518 0.616 - 0.821: 42 0.821 - 1.027: 14 Chirality restraints: 7406 Sorted by residual: chirality pdb=" CB ILE W 178 " pdb=" CA ILE W 178 " pdb=" CG1 ILE W 178 " pdb=" CG2 ILE W 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CB ILE M 178 " pdb=" CA ILE M 178 " pdb=" CG1 ILE M 178 " pdb=" CG2 ILE M 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CB ILE V 178 " pdb=" CA ILE V 178 " pdb=" CG1 ILE V 178 " pdb=" CG2 ILE V 178 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 7403 not shown) Planarity restraints: 8106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 124 " -0.151 2.00e-02 2.50e+03 1.18e-01 2.76e+02 pdb=" CG TYR 2 124 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 124 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 124 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 124 " 0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 124 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR 2 124 " 0.070 2.00e-02 2.50e+03 pdb=" OH TYR 2 124 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 124 " -0.151 2.00e-02 2.50e+03 1.17e-01 2.76e+02 pdb=" CG TYR K 124 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR K 124 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR K 124 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR K 124 " 0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR K 124 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR K 124 " 0.070 2.00e-02 2.50e+03 pdb=" OH TYR K 124 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR X 124 " 0.150 2.00e-02 2.50e+03 1.17e-01 2.76e+02 pdb=" CG TYR X 124 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR X 124 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR X 124 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR X 124 " -0.093 2.00e-02 2.50e+03 pdb=" CE2 TYR X 124 " -0.095 2.00e-02 2.50e+03 pdb=" CZ TYR X 124 " -0.070 2.00e-02 2.50e+03 pdb=" OH TYR X 124 " 0.220 2.00e-02 2.50e+03 ... (remaining 8103 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 487 2.52 - 3.11: 31577 3.11 - 3.71: 70632 3.71 - 4.30: 106955 4.30 - 4.90: 178413 Nonbonded interactions: 388064 Sorted by model distance: nonbonded pdb=" OXT LEU Z 203 " pdb=" OXT LEU M 203 " model vdw 1.922 3.040 nonbonded pdb=" OXT LEU I 203 " pdb=" OXT LEU W 203 " model vdw 1.922 3.040 nonbonded pdb=" OXT LEU N 203 " pdb=" OXT LEU Y 203 " model vdw 1.923 3.040 nonbonded pdb=" OXT LEU 2 203 " pdb=" OXT LEU K 203 " model vdw 1.923 3.040 nonbonded pdb=" OXT LEU V 203 " pdb=" OXT LEU J 203 " model vdw 1.923 3.040 ... (remaining 388059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'S' selection = chain 'F' selection = chain 'T' selection = chain 'G' selection = chain 'U' selection = chain 'A' selection = chain 'O' selection = chain 'B' selection = chain 'P' selection = chain 'C' selection = chain 'Q' selection = chain 'D' selection = chain 'R' selection = chain 'E' } ncs_group { reference = chain 'Z' selection = chain 'M' selection = chain '1' selection = chain 'N' selection = chain '2' selection = chain 'H' selection = chain 'V' selection = chain 'I' selection = chain 'W' selection = chain 'J' selection = chain 'X' selection = chain 'K' selection = chain 'Y' selection = chain 'L' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 40.730 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.034 0.147 46816 Z= 2.273 Angle : 3.609 15.587 63182 Z= 2.428 Chirality : 0.229 1.027 7406 Planarity : 0.030 0.246 8106 Dihedral : 18.099 127.392 17682 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 1.89 % Allowed : 8.04 % Favored : 90.07 % Rotamer: Outliers : 9.27 % Allowed : 12.08 % Favored : 78.65 % Cbeta Deviations : 10.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.09), residues: 5922 helix: -2.41 (0.09), residues: 2226 sheet: -0.96 (0.14), residues: 1302 loop : -3.12 (0.10), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.011 ARG O 20 TYR 0.220 0.047 TYR 2 124 PHE 0.146 0.046 PHE T 91 HIS 0.020 0.009 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.03437 (46816) covalent geometry : angle 3.60881 (63182) hydrogen bonds : bond 0.23728 ( 2733) hydrogen bonds : angle 8.58828 ( 7821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2360 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 462 poor density : 1898 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 76 ILE cc_start: 0.9082 (mm) cc_final: 0.8877 (mm) REVERT: Z 149 ASP cc_start: 0.5737 (m-30) cc_final: 0.5453 (m-30) REVERT: Z 203 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.1616 (tp) REVERT: F 221 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.5884 (t80) REVERT: T 53 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4555 (mmmt) REVERT: T 221 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6952 (t80) REVERT: 1 45 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7780 (mp) REVERT: 1 85 ASN cc_start: 0.8506 (m110) cc_final: 0.8144 (m110) REVERT: 1 149 ASP cc_start: 0.6079 (m-30) cc_final: 0.5763 (m-30) REVERT: 1 203 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2066 (tp) REVERT: G 53 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4922 (mmmt) REVERT: G 158 ASN cc_start: 0.7970 (m110) cc_final: 0.7723 (m-40) REVERT: N 112 SER cc_start: 0.8544 (t) cc_final: 0.8332 (p) REVERT: N 131 SER cc_start: 0.8699 (t) cc_final: 0.8426 (t) REVERT: N 149 ASP cc_start: 0.5982 (m-30) cc_final: 0.5585 (m-30) REVERT: N 203 LEU cc_start: 0.0891 (OUTLIER) cc_final: 0.0664 (tp) REVERT: U 225 ASP cc_start: 0.4295 (OUTLIER) cc_final: 0.3014 (p0) REVERT: 2 203 LEU cc_start: 0.1751 (OUTLIER) cc_final: 0.1332 (tp) REVERT: A 53 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4758 (mmmt) REVERT: A 225 ASP cc_start: 0.4182 (OUTLIER) cc_final: 0.3348 (p0) REVERT: H 112 SER cc_start: 0.8587 (t) cc_final: 0.8299 (p) REVERT: H 114 ASP cc_start: 0.8079 (p0) cc_final: 0.7788 (p0) REVERT: O 90 ASP cc_start: 0.6558 (m-30) cc_final: 0.6347 (m-30) REVERT: O 221 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.6923 (t80) REVERT: O 225 ASP cc_start: 0.4272 (OUTLIER) cc_final: 0.2795 (p0) REVERT: V 120 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8588 (t) REVERT: V 149 ASP cc_start: 0.5939 (m-30) cc_final: 0.5663 (m-30) REVERT: I 149 ASP cc_start: 0.5734 (m-30) cc_final: 0.5446 (m-30) REVERT: I 203 LEU cc_start: 0.2009 (OUTLIER) cc_final: 0.1616 (tp) REVERT: P 221 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.5854 (t80) REVERT: C 53 LYS cc_start: 0.4750 (OUTLIER) cc_final: 0.4529 (mmmt) REVERT: C 221 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6965 (t80) REVERT: J 45 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7764 (mp) REVERT: J 85 ASN cc_start: 0.8460 (m110) cc_final: 0.8118 (m110) REVERT: J 149 ASP cc_start: 0.6090 (m-30) cc_final: 0.5757 (m-30) REVERT: J 203 LEU cc_start: 0.2336 (OUTLIER) cc_final: 0.2076 (tp) REVERT: Q 53 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4930 (mmmt) REVERT: Q 118 ASP cc_start: 0.7535 (m-30) cc_final: 0.7305 (m-30) REVERT: Q 158 ASN cc_start: 0.7956 (m110) cc_final: 0.7719 (m-40) REVERT: X 112 SER cc_start: 0.8537 (t) cc_final: 0.8325 (p) REVERT: X 131 SER cc_start: 0.8711 (t) cc_final: 0.8446 (t) REVERT: X 149 ASP cc_start: 0.5987 (m-30) cc_final: 0.5591 (m-30) REVERT: X 203 LEU cc_start: 0.0900 (OUTLIER) cc_final: 0.0670 (tp) REVERT: D 225 ASP cc_start: 0.4306 (OUTLIER) cc_final: 0.2997 (p0) REVERT: K 203 LEU cc_start: 0.1758 (OUTLIER) cc_final: 0.1334 (tp) REVERT: R 225 ASP cc_start: 0.4154 (OUTLIER) cc_final: 0.3349 (p0) REVERT: Y 112 SER cc_start: 0.8576 (t) cc_final: 0.8288 (p) REVERT: Y 114 ASP cc_start: 0.8053 (p0) cc_final: 0.7769 (p0) REVERT: E 221 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6945 (t80) REVERT: L 120 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (t) REVERT: L 149 ASP cc_start: 0.5916 (m-30) cc_final: 0.5652 (m-30) outliers start: 462 outliers final: 194 residues processed: 2210 average time/residue: 0.3169 time to fit residues: 1125.8573 Evaluate side-chains 1528 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1306 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 136 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 136 LEU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 224 TYR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 37 ILE Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 136 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 224 TYR Chi-restraints excluded: chain U residue 225 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 136 LEU Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 121 GLN S 219 ASN Z 85 ASN Z 89 GLN Z 141 GLN Z 191 GLN F 119 GLN F 121 GLN F 219 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 GLN T 111 ASN T 121 GLN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 122 GLN N 191 GLN U 121 GLN 2 191 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN O 111 ASN O 119 GLN O 121 GLN O 219 ASN V 98 GLN B 121 GLN B 219 ASN I 85 ASN I 89 GLN I 141 GLN I 191 GLN P 119 GLN P 121 GLN P 219 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 191 GLN C 111 ASN C 121 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Q 122 GLN X 191 GLN D 121 GLN K 191 GLN ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 GLN Y 191 GLN E 111 ASN E 119 GLN E 121 GLN E 219 ASN L 98 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.082364 restraints weight = 71359.893| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.32 r_work: 0.2752 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 46816 Z= 0.276 Angle : 0.848 11.123 63182 Z= 0.469 Chirality : 0.054 0.251 7406 Planarity : 0.006 0.070 8106 Dihedral : 9.938 102.027 6926 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.71 % Favored : 95.81 % Rotamer: Outliers : 7.42 % Allowed : 18.92 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.10), residues: 5922 helix: 0.66 (0.10), residues: 2366 sheet: -0.33 (0.12), residues: 1344 loop : -2.92 (0.10), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 55 TYR 0.025 0.003 TYR W 92 PHE 0.024 0.003 PHE R 42 HIS 0.012 0.005 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00621 (46816) covalent geometry : angle 0.84788 (63182) hydrogen bonds : bond 0.04777 ( 2733) hydrogen bonds : angle 5.63415 ( 7821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1650 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 370 poor density : 1280 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 115 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (ttm110) REVERT: S 123 TYR cc_start: 0.9292 (m-80) cc_final: 0.9071 (m-80) REVERT: S 142 ASP cc_start: 0.8690 (p0) cc_final: 0.8393 (p0) REVERT: S 221 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7183 (t80) REVERT: Z 17 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8539 (pp20) REVERT: Z 96 MET cc_start: 0.8930 (mpp) cc_final: 0.8373 (mpp) REVERT: Z 150 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8434 (mt-10) REVERT: Z 181 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8459 (ptmm) REVERT: F 221 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.5287 (t80) REVERT: M 58 TYR cc_start: 0.8764 (t80) cc_final: 0.8427 (t80) REVERT: T 44 ASN cc_start: 0.8703 (m-40) cc_final: 0.8427 (m110) REVERT: T 53 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5938 (mmmt) REVERT: T 197 LEU cc_start: 0.9662 (tp) cc_final: 0.9234 (tp) REVERT: T 221 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.6611 (t80) REVERT: T 232 PHE cc_start: 0.8161 (m-80) cc_final: 0.7469 (m-80) REVERT: 1 14 MET cc_start: 0.9114 (mtm) cc_final: 0.8884 (mtp) REVERT: 1 193 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7763 (mt-10) REVERT: G 53 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6275 (mmmt) REVERT: G 118 ASP cc_start: 0.8810 (m-30) cc_final: 0.8568 (m-30) REVERT: G 221 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7160 (t80) REVERT: N 14 MET cc_start: 0.9070 (mtm) cc_final: 0.8779 (mtp) REVERT: N 71 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8485 (mpp80) REVERT: N 193 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7551 (mt-10) REVERT: 2 14 MET cc_start: 0.9060 (mtm) cc_final: 0.8837 (mtp) REVERT: 2 17 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: 2 190 ASP cc_start: 0.8512 (m-30) cc_final: 0.8218 (m-30) REVERT: A 53 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6297 (mmmt) REVERT: A 99 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 123 TYR cc_start: 0.9276 (m-80) cc_final: 0.9060 (m-80) REVERT: A 191 THR cc_start: 0.9354 (m) cc_final: 0.9107 (m) REVERT: A 197 LEU cc_start: 0.9569 (tp) cc_final: 0.9214 (tp) REVERT: A 221 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 232 PHE cc_start: 0.8149 (m-80) cc_final: 0.7463 (m-80) REVERT: H 51 ASP cc_start: 0.8784 (m-30) cc_final: 0.8446 (m-30) REVERT: H 55 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.8667 (mm) REVERT: H 58 TYR cc_start: 0.8775 (t80) cc_final: 0.8415 (t80) REVERT: H 62 GLU cc_start: 0.8945 (tp30) cc_final: 0.8681 (tp30) REVERT: H 139 GLU cc_start: 0.8933 (tp30) cc_final: 0.8570 (tp30) REVERT: H 193 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7716 (mt-10) REVERT: O 142 ASP cc_start: 0.8619 (p0) cc_final: 0.8262 (p0) REVERT: O 150 ASP cc_start: 0.8641 (t70) cc_final: 0.8259 (t0) REVERT: O 221 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7169 (t80) REVERT: O 225 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (p0) REVERT: V 17 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: V 149 ASP cc_start: 0.8462 (m-30) cc_final: 0.8256 (m-30) REVERT: V 181 LYS cc_start: 0.8874 (ttpp) cc_final: 0.7954 (pttp) REVERT: V 190 ASP cc_start: 0.8300 (m-30) cc_final: 0.7928 (m-30) REVERT: B 115 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (ttm110) REVERT: B 123 TYR cc_start: 0.9295 (m-80) cc_final: 0.9066 (m-80) REVERT: B 142 ASP cc_start: 0.8702 (p0) cc_final: 0.8411 (p0) REVERT: B 221 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7185 (t80) REVERT: I 17 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8533 (pp20) REVERT: I 96 MET cc_start: 0.8923 (mpp) cc_final: 0.8367 (mpp) REVERT: I 150 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8435 (mt-10) REVERT: I 181 LYS cc_start: 0.8714 (ptpp) cc_final: 0.8447 (ptmm) REVERT: P 221 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.5282 (t80) REVERT: W 58 TYR cc_start: 0.8765 (t80) cc_final: 0.8432 (t80) REVERT: W 93 MET cc_start: 0.8682 (mmm) cc_final: 0.8451 (mmt) REVERT: C 44 ASN cc_start: 0.8714 (m-40) cc_final: 0.8443 (m110) REVERT: C 53 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.5946 (mmmt) REVERT: C 197 LEU cc_start: 0.9664 (tp) cc_final: 0.9238 (tp) REVERT: C 221 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.6616 (t80) REVERT: C 232 PHE cc_start: 0.8168 (m-80) cc_final: 0.7474 (m-80) REVERT: J 14 MET cc_start: 0.9102 (mtm) cc_final: 0.8877 (mtp) REVERT: J 193 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7750 (mt-10) REVERT: Q 44 ASN cc_start: 0.8608 (m-40) cc_final: 0.8408 (m110) REVERT: Q 53 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6284 (mmmt) REVERT: Q 118 ASP cc_start: 0.8907 (m-30) cc_final: 0.8585 (m-30) REVERT: Q 221 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7158 (t80) REVERT: X 14 MET cc_start: 0.9069 (mtm) cc_final: 0.8780 (mtp) REVERT: X 71 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (mpp80) REVERT: X 193 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7547 (mt-10) REVERT: K 14 MET cc_start: 0.9050 (mtm) cc_final: 0.8823 (mtp) REVERT: K 17 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8336 (pp20) REVERT: K 190 ASP cc_start: 0.8509 (m-30) cc_final: 0.8212 (m-30) REVERT: R 99 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8151 (mm-30) REVERT: R 123 TYR cc_start: 0.9270 (m-80) cc_final: 0.9049 (m-80) REVERT: R 191 THR cc_start: 0.9356 (m) cc_final: 0.9117 (m) REVERT: R 197 LEU cc_start: 0.9565 (tp) cc_final: 0.9213 (tp) REVERT: R 221 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7473 (t80) REVERT: R 232 PHE cc_start: 0.8159 (m-80) cc_final: 0.7472 (m-80) REVERT: Y 51 ASP cc_start: 0.8778 (m-30) cc_final: 0.8438 (m-30) REVERT: Y 55 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8661 (mm) REVERT: Y 58 TYR cc_start: 0.8787 (t80) cc_final: 0.8424 (t80) REVERT: Y 62 GLU cc_start: 0.8945 (tp30) cc_final: 0.8682 (tp30) REVERT: Y 139 GLU cc_start: 0.8949 (tp30) cc_final: 0.8590 (tp30) REVERT: Y 193 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 142 ASP cc_start: 0.8617 (p0) cc_final: 0.8262 (p0) REVERT: E 150 ASP cc_start: 0.8622 (t70) cc_final: 0.8236 (t0) REVERT: E 221 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7275 (t80) REVERT: E 225 ASP cc_start: 0.8015 (t70) cc_final: 0.7392 (p0) REVERT: L 17 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8403 (pp20) REVERT: L 149 ASP cc_start: 0.8445 (m-30) cc_final: 0.8235 (m-30) REVERT: L 181 LYS cc_start: 0.8877 (ttpp) cc_final: 0.7960 (pttp) REVERT: L 190 ASP cc_start: 0.8292 (m-30) cc_final: 0.7915 (m-30) outliers start: 370 outliers final: 245 residues processed: 1576 average time/residue: 0.2633 time to fit residues: 691.2932 Evaluate side-chains 1357 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 1082 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 115 ARG Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 37 ILE Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 179 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 179 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 55 LEU Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 62 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 344 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 186 GLN Z 191 GLN F 44 ASN 1 186 GLN 1 191 GLN U 119 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN O 122 GLN I 186 GLN I 191 GLN P 44 ASN C 122 GLN J 186 GLN J 191 GLN D 119 GLN Y 191 GLN E 111 ASN E 122 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.084750 restraints weight = 70467.366| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.31 r_work: 0.2785 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46816 Z= 0.150 Angle : 0.686 8.440 63182 Z= 0.379 Chirality : 0.046 0.190 7406 Planarity : 0.005 0.061 8106 Dihedral : 8.657 102.292 6828 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.12 % Rotamer: Outliers : 6.54 % Allowed : 20.73 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.10), residues: 5922 helix: 1.86 (0.11), residues: 2324 sheet: -0.24 (0.12), residues: 1372 loop : -2.59 (0.10), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 57 TYR 0.015 0.002 TYR M 92 PHE 0.019 0.002 PHE P 232 HIS 0.014 0.004 HIS 2 28 Details of bonding type rmsd covalent geometry : bond 0.00337 (46816) covalent geometry : angle 0.68619 (63182) hydrogen bonds : bond 0.03834 ( 2733) hydrogen bonds : angle 5.07746 ( 7821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1574 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 1248 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 ASN cc_start: 0.8489 (t0) cc_final: 0.8228 (t0) REVERT: S 221 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7131 (t80) REVERT: S 227 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: Z 17 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: Z 62 GLU cc_start: 0.8778 (tp30) cc_final: 0.8573 (mm-30) REVERT: Z 96 MET cc_start: 0.8864 (mpp) cc_final: 0.8369 (mpp) REVERT: Z 144 GLU cc_start: 0.8531 (pm20) cc_final: 0.8291 (pm20) REVERT: F 221 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.5465 (t80) REVERT: M 58 TYR cc_start: 0.8829 (t80) cc_final: 0.8437 (t80) REVERT: M 93 MET cc_start: 0.8760 (mmt) cc_final: 0.8347 (mmm) REVERT: T 44 ASN cc_start: 0.8664 (m-40) cc_final: 0.8438 (m110) REVERT: T 53 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6085 (tptp) REVERT: T 221 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.6505 (t80) REVERT: T 225 ASP cc_start: 0.7846 (t70) cc_final: 0.7461 (t70) REVERT: T 227 GLU cc_start: 0.8337 (pm20) cc_final: 0.7975 (pm20) REVERT: T 232 PHE cc_start: 0.8130 (m-80) cc_final: 0.7520 (m-80) REVERT: 1 17 GLU cc_start: 0.8856 (pm20) cc_final: 0.8520 (pm20) REVERT: 1 193 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7749 (mt-10) REVERT: G 53 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6293 (mmmt) REVERT: G 99 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8142 (mm-30) REVERT: G 118 ASP cc_start: 0.8755 (m-30) cc_final: 0.8423 (m-30) REVERT: G 186 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: G 221 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7111 (t80) REVERT: G 225 ASP cc_start: 0.8049 (p0) cc_final: 0.7480 (p0) REVERT: N 17 GLU cc_start: 0.8717 (pm20) cc_final: 0.8367 (pm20) REVERT: N 193 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7753 (mt-10) REVERT: U 90 ASP cc_start: 0.8572 (m-30) cc_final: 0.8240 (m-30) REVERT: U 99 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7914 (mm-30) REVERT: 2 17 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: 2 190 ASP cc_start: 0.8370 (m-30) cc_final: 0.8155 (m-30) REVERT: 2 191 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 53 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6595 (mmmt) REVERT: A 99 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 156 THR cc_start: 0.9389 (m) cc_final: 0.9079 (p) REVERT: A 191 THR cc_start: 0.9344 (m) cc_final: 0.9000 (m) REVERT: A 221 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 232 PHE cc_start: 0.8237 (m-80) cc_final: 0.7511 (m-80) REVERT: H 55 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.8775 (mm) REVERT: H 58 TYR cc_start: 0.8787 (t80) cc_final: 0.8263 (t80) REVERT: H 62 GLU cc_start: 0.8880 (tp30) cc_final: 0.8665 (tp30) REVERT: H 139 GLU cc_start: 0.8791 (tp30) cc_final: 0.8493 (tp30) REVERT: H 145 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8610 (mtpp) REVERT: H 146 MET cc_start: 0.8800 (mtp) cc_final: 0.8560 (mtp) REVERT: H 153 ASP cc_start: 0.8718 (m-30) cc_final: 0.8413 (m-30) REVERT: O 150 ASP cc_start: 0.8550 (t70) cc_final: 0.8170 (t0) REVERT: O 221 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7540 (t80) REVERT: O 225 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7969 (p0) REVERT: V 17 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8345 (pp20) REVERT: V 62 GLU cc_start: 0.8763 (tp30) cc_final: 0.8537 (mm-30) REVERT: V 145 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8626 (mtpp) REVERT: V 186 GLN cc_start: 0.8557 (tt0) cc_final: 0.8283 (tp-100) REVERT: V 190 ASP cc_start: 0.8267 (m-30) cc_final: 0.8000 (m-30) REVERT: V 191 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 111 ASN cc_start: 0.8480 (t0) cc_final: 0.8222 (t0) REVERT: B 221 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7133 (t80) REVERT: B 227 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: I 17 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: I 62 GLU cc_start: 0.8779 (tp30) cc_final: 0.8574 (mm-30) REVERT: I 96 MET cc_start: 0.8874 (mpp) cc_final: 0.8382 (mpp) REVERT: I 144 GLU cc_start: 0.8525 (pm20) cc_final: 0.8282 (pm20) REVERT: P 221 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.5473 (t80) REVERT: W 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8438 (t80) REVERT: W 93 MET cc_start: 0.8774 (mmm) cc_final: 0.8397 (mmm) REVERT: C 44 ASN cc_start: 0.8668 (m-40) cc_final: 0.8444 (m110) REVERT: C 53 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6077 (tptp) REVERT: C 221 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.6491 (t80) REVERT: C 225 ASP cc_start: 0.7831 (t70) cc_final: 0.7446 (t70) REVERT: C 227 GLU cc_start: 0.8325 (pm20) cc_final: 0.7963 (pm20) REVERT: C 232 PHE cc_start: 0.8133 (m-80) cc_final: 0.7554 (m-80) REVERT: J 17 GLU cc_start: 0.8855 (pm20) cc_final: 0.8546 (pm20) REVERT: J 193 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7749 (mt-10) REVERT: Q 53 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6299 (mmmt) REVERT: Q 99 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8147 (mm-30) REVERT: Q 118 ASP cc_start: 0.8920 (m-30) cc_final: 0.8540 (m-30) REVERT: Q 221 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7098 (t80) REVERT: Q 225 ASP cc_start: 0.8053 (p0) cc_final: 0.7500 (p0) REVERT: X 17 GLU cc_start: 0.8722 (pm20) cc_final: 0.8368 (pm20) REVERT: X 193 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 90 ASP cc_start: 0.8590 (m-30) cc_final: 0.8260 (m-30) REVERT: D 99 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7903 (mm-30) REVERT: K 17 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8225 (pp20) REVERT: K 190 ASP cc_start: 0.8372 (m-30) cc_final: 0.8159 (m-30) REVERT: K 191 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7378 (tm-30) REVERT: R 22 PHE cc_start: 0.9096 (m-80) cc_final: 0.8854 (m-10) REVERT: R 99 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7987 (mm-30) REVERT: R 156 THR cc_start: 0.9392 (m) cc_final: 0.9086 (p) REVERT: R 191 THR cc_start: 0.9345 (m) cc_final: 0.9002 (m) REVERT: R 221 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7525 (t80) REVERT: R 232 PHE cc_start: 0.8237 (m-80) cc_final: 0.7507 (m-80) REVERT: Y 55 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.8771 (mm) REVERT: Y 58 TYR cc_start: 0.8792 (t80) cc_final: 0.8274 (t80) REVERT: Y 62 GLU cc_start: 0.8895 (tp30) cc_final: 0.8688 (tp30) REVERT: Y 114 ASP cc_start: 0.9191 (p0) cc_final: 0.8980 (p0) REVERT: Y 139 GLU cc_start: 0.8809 (tp30) cc_final: 0.8512 (tp30) REVERT: Y 145 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8618 (mtpp) REVERT: Y 146 MET cc_start: 0.8822 (mtp) cc_final: 0.8582 (mtp) REVERT: Y 153 ASP cc_start: 0.8706 (m-30) cc_final: 0.8400 (m-30) REVERT: E 150 ASP cc_start: 0.8543 (t70) cc_final: 0.8161 (t0) REVERT: E 221 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7491 (t80) REVERT: E 225 ASP cc_start: 0.7872 (t70) cc_final: 0.7497 (t70) REVERT: E 227 GLU cc_start: 0.8274 (pm20) cc_final: 0.7787 (pm20) REVERT: L 17 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8362 (pp20) REVERT: L 62 GLU cc_start: 0.8758 (tp30) cc_final: 0.8535 (mm-30) REVERT: L 120 VAL cc_start: 0.9626 (OUTLIER) cc_final: 0.9412 (p) REVERT: L 145 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8635 (mtpp) REVERT: L 186 GLN cc_start: 0.8586 (tt0) cc_final: 0.8304 (tp-100) REVERT: L 190 ASP cc_start: 0.8273 (m-30) cc_final: 0.8000 (m-30) REVERT: L 191 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 326 outliers final: 216 residues processed: 1491 average time/residue: 0.2805 time to fit residues: 699.6015 Evaluate side-chains 1383 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1137 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 227 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 143 SER Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 186 GLN Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 252 optimal weight: 0.0970 chunk 502 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 536 optimal weight: 0.9980 chunk 396 optimal weight: 9.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 44 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 186 GLN G 122 GLN H 191 GLN O 122 GLN P 44 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN Q 122 GLN Y 191 GLN E 122 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.083717 restraints weight = 70627.876| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.33 r_work: 0.2785 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46816 Z= 0.151 Angle : 0.662 9.179 63182 Z= 0.362 Chirality : 0.045 0.192 7406 Planarity : 0.005 0.058 8106 Dihedral : 8.078 102.654 6761 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.21 % Favored : 96.56 % Rotamer: Outliers : 7.16 % Allowed : 20.83 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.10), residues: 5922 helix: 2.05 (0.11), residues: 2352 sheet: -0.34 (0.12), residues: 1372 loop : -2.34 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 57 TYR 0.013 0.001 TYR Z 92 PHE 0.018 0.002 PHE A 42 HIS 0.009 0.004 HIS 2 28 Details of bonding type rmsd covalent geometry : bond 0.00352 (46816) covalent geometry : angle 0.66243 (63182) hydrogen bonds : bond 0.03532 ( 2733) hydrogen bonds : angle 4.90984 ( 7821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 357 poor density : 1214 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.7101 (t80) REVERT: S 232 PHE cc_start: 0.8161 (m-80) cc_final: 0.7744 (m-80) REVERT: Z 14 MET cc_start: 0.8958 (mtp) cc_final: 0.8751 (mtp) REVERT: Z 17 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8455 (pp20) REVERT: Z 96 MET cc_start: 0.8850 (mpp) cc_final: 0.8358 (mpp) REVERT: F 221 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.5506 (t80) REVERT: M 58 TYR cc_start: 0.8832 (t80) cc_final: 0.8502 (t80) REVERT: M 93 MET cc_start: 0.8718 (mmt) cc_final: 0.8301 (mmm) REVERT: M 173 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9023 (mt) REVERT: M 191 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7602 (tm-30) REVERT: T 44 ASN cc_start: 0.8638 (m-40) cc_final: 0.8421 (m110) REVERT: T 53 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6296 (tptp) REVERT: T 61 GLN cc_start: 0.8231 (mt0) cc_final: 0.8016 (tt0) REVERT: T 221 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.6875 (t80) REVERT: T 225 ASP cc_start: 0.8070 (t70) cc_final: 0.7739 (t70) REVERT: T 227 GLU cc_start: 0.8452 (pm20) cc_final: 0.8090 (pm20) REVERT: T 232 PHE cc_start: 0.8192 (m-80) cc_final: 0.7657 (m-80) REVERT: 1 17 GLU cc_start: 0.8784 (pm20) cc_final: 0.8514 (pm20) REVERT: 1 139 GLU cc_start: 0.8760 (tp30) cc_final: 0.8440 (tp30) REVERT: 1 141 GLN cc_start: 0.8841 (mt0) cc_final: 0.8626 (mt0) REVERT: 1 182 ASP cc_start: 0.8458 (m-30) cc_final: 0.8228 (t0) REVERT: 1 191 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7441 (tm-30) REVERT: 1 193 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7774 (mt-10) REVERT: G 142 ASP cc_start: 0.8441 (p0) cc_final: 0.8053 (p0) REVERT: G 221 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7183 (t80) REVERT: G 232 PHE cc_start: 0.8250 (m-80) cc_final: 0.7958 (m-80) REVERT: N 17 GLU cc_start: 0.8683 (pm20) cc_final: 0.8300 (pm20) REVERT: N 139 GLU cc_start: 0.8687 (tp30) cc_final: 0.8337 (tp30) REVERT: N 193 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7813 (mt-10) REVERT: U 99 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7860 (mm-30) REVERT: 2 17 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: 2 150 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8554 (mt-10) REVERT: 2 191 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 53 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6697 (mmmt) REVERT: A 123 TYR cc_start: 0.9386 (m-80) cc_final: 0.9158 (m-80) REVERT: A 156 THR cc_start: 0.9417 (m) cc_final: 0.9153 (p) REVERT: A 191 THR cc_start: 0.9399 (m) cc_final: 0.9018 (m) REVERT: A 221 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7413 (t80) REVERT: A 232 PHE cc_start: 0.8259 (m-80) cc_final: 0.7486 (m-80) REVERT: H 55 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8699 (mm) REVERT: H 58 TYR cc_start: 0.8815 (t80) cc_final: 0.8276 (t80) REVERT: H 145 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8576 (mtpp) REVERT: H 146 MET cc_start: 0.8744 (mtp) cc_final: 0.8512 (mtp) REVERT: H 153 ASP cc_start: 0.8780 (m-30) cc_final: 0.8412 (m-30) REVERT: O 150 ASP cc_start: 0.8552 (t70) cc_final: 0.8170 (t0) REVERT: O 221 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7547 (t80) REVERT: O 225 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7524 (p0) REVERT: V 17 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: V 62 GLU cc_start: 0.8817 (tp30) cc_final: 0.8577 (mm-30) REVERT: V 191 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7716 (tt0) REVERT: V 193 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7682 (mt-10) REVERT: B 221 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 232 PHE cc_start: 0.8171 (m-80) cc_final: 0.7749 (m-80) REVERT: I 17 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: I 96 MET cc_start: 0.8863 (mpp) cc_final: 0.8375 (mpp) REVERT: P 221 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.5513 (t80) REVERT: W 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8499 (t80) REVERT: W 93 MET cc_start: 0.8647 (mmm) cc_final: 0.8277 (mmm) REVERT: W 173 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9023 (mt) REVERT: W 191 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 44 ASN cc_start: 0.8647 (m-40) cc_final: 0.8424 (m110) REVERT: C 53 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6304 (tptp) REVERT: C 191 THR cc_start: 0.9239 (m) cc_final: 0.9015 (p) REVERT: C 221 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.6866 (t80) REVERT: C 225 ASP cc_start: 0.8068 (t70) cc_final: 0.7737 (t70) REVERT: C 227 GLU cc_start: 0.8441 (pm20) cc_final: 0.8080 (pm20) REVERT: C 232 PHE cc_start: 0.7990 (m-80) cc_final: 0.7315 (m-80) REVERT: J 17 GLU cc_start: 0.8779 (pm20) cc_final: 0.8507 (pm20) REVERT: J 139 GLU cc_start: 0.8752 (tp30) cc_final: 0.8432 (tp30) REVERT: J 141 GLN cc_start: 0.8846 (mt0) cc_final: 0.8625 (mt0) REVERT: J 182 ASP cc_start: 0.8482 (m-30) cc_final: 0.8243 (t0) REVERT: J 191 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7425 (tm-30) REVERT: J 193 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7765 (mt-10) REVERT: Q 118 ASP cc_start: 0.8988 (m-30) cc_final: 0.8642 (m-30) REVERT: Q 142 ASP cc_start: 0.8453 (p0) cc_final: 0.8068 (p0) REVERT: Q 221 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7177 (t80) REVERT: Q 232 PHE cc_start: 0.8130 (m-80) cc_final: 0.7809 (m-80) REVERT: X 17 GLU cc_start: 0.8697 (pm20) cc_final: 0.8312 (pm20) REVERT: X 139 GLU cc_start: 0.8696 (tp30) cc_final: 0.8341 (tp30) REVERT: X 193 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7812 (mt-10) REVERT: D 90 ASP cc_start: 0.8579 (m-30) cc_final: 0.8229 (m-30) REVERT: D 99 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7864 (mm-30) REVERT: K 17 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: K 150 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8585 (mt-10) REVERT: K 191 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7438 (tm-30) REVERT: R 123 TYR cc_start: 0.9381 (m-80) cc_final: 0.9146 (m-80) REVERT: R 156 THR cc_start: 0.9415 (m) cc_final: 0.9149 (p) REVERT: R 191 THR cc_start: 0.9408 (m) cc_final: 0.9030 (m) REVERT: R 221 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7402 (t80) REVERT: R 232 PHE cc_start: 0.8271 (m-80) cc_final: 0.7484 (m-80) REVERT: Y 55 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8699 (mm) REVERT: Y 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8296 (t80) REVERT: Y 145 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8582 (mtpp) REVERT: Y 146 MET cc_start: 0.8767 (mtp) cc_final: 0.8542 (mtp) REVERT: Y 153 ASP cc_start: 0.8792 (m-30) cc_final: 0.8432 (m-30) REVERT: E 150 ASP cc_start: 0.8526 (t70) cc_final: 0.8143 (t0) REVERT: E 221 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7548 (t80) REVERT: E 225 ASP cc_start: 0.7783 (t70) cc_final: 0.7337 (t0) REVERT: E 227 GLU cc_start: 0.8259 (pm20) cc_final: 0.7912 (pm20) REVERT: L 17 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: L 62 GLU cc_start: 0.8818 (tp30) cc_final: 0.8577 (mm-30) REVERT: L 191 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7720 (tt0) REVERT: L 193 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7686 (mt-10) outliers start: 357 outliers final: 239 residues processed: 1468 average time/residue: 0.2736 time to fit residues: 679.7559 Evaluate side-chains 1372 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 1107 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 53 LYS Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 7 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 137 VAL Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 143 SER Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 137 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 137 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 55 optimal weight: 0.9990 chunk 550 optimal weight: 0.7980 chunk 429 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 472 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 ASN Z 186 GLN T 111 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 122 GLN A 111 ASN H 141 GLN H 191 GLN O 122 GLN I 85 ASN I 186 GLN C 111 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 ASN Q 122 GLN R 111 ASN Y 191 GLN E 122 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.085128 restraints weight = 70221.670| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.34 r_work: 0.2803 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46816 Z= 0.133 Angle : 0.647 9.534 63182 Z= 0.353 Chirality : 0.044 0.188 7406 Planarity : 0.005 0.054 8106 Dihedral : 7.745 101.386 6746 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.44 % Favored : 96.32 % Rotamer: Outliers : 6.68 % Allowed : 22.41 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.11), residues: 5922 helix: 2.25 (0.11), residues: 2380 sheet: -0.37 (0.12), residues: 1372 loop : -2.33 (0.11), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 57 TYR 0.023 0.001 TYR Y 95 PHE 0.015 0.001 PHE S 232 HIS 0.008 0.003 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00298 (46816) covalent geometry : angle 0.64747 (63182) hydrogen bonds : bond 0.03234 ( 2733) hydrogen bonds : angle 4.80529 ( 7821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 333 poor density : 1228 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7210 (t80) REVERT: S 232 PHE cc_start: 0.8170 (m-80) cc_final: 0.7915 (m-80) REVERT: Z 14 MET cc_start: 0.8942 (mtp) cc_final: 0.8711 (mtp) REVERT: Z 17 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8409 (pp20) REVERT: Z 96 MET cc_start: 0.8861 (mpp) cc_final: 0.8385 (mpp) REVERT: Z 191 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7145 (tm-30) REVERT: F 68 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (mm-40) REVERT: F 221 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.5601 (t80) REVERT: F 225 ASP cc_start: 0.8062 (t0) cc_final: 0.7219 (t0) REVERT: F 227 GLU cc_start: 0.8201 (pm20) cc_final: 0.7894 (pm20) REVERT: M 58 TYR cc_start: 0.8848 (t80) cc_final: 0.8513 (t80) REVERT: M 93 MET cc_start: 0.8667 (mmt) cc_final: 0.8405 (mmm) REVERT: M 173 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (mt) REVERT: M 185 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9015 (m) REVERT: T 44 ASN cc_start: 0.8721 (m-40) cc_final: 0.8518 (m110) REVERT: T 61 GLN cc_start: 0.8234 (mt0) cc_final: 0.8003 (tt0) REVERT: T 221 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.6901 (t80) REVERT: T 225 ASP cc_start: 0.8142 (t70) cc_final: 0.7535 (t70) REVERT: T 227 GLU cc_start: 0.8455 (pm20) cc_final: 0.7874 (pm20) REVERT: T 232 PHE cc_start: 0.8224 (m-80) cc_final: 0.7939 (m-80) REVERT: 1 17 GLU cc_start: 0.8695 (pm20) cc_final: 0.8420 (pm20) REVERT: 1 58 TYR cc_start: 0.8809 (t80) cc_final: 0.8498 (t80) REVERT: 1 93 MET cc_start: 0.8430 (mmt) cc_final: 0.8179 (mmm) REVERT: 1 193 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7760 (mt-10) REVERT: G 118 ASP cc_start: 0.8784 (m-30) cc_final: 0.8468 (m-30) REVERT: G 156 THR cc_start: 0.9341 (m) cc_final: 0.9090 (p) REVERT: G 221 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.7292 (t80) REVERT: N 8 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8837 (pp) REVERT: N 17 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: 2 17 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8158 (pp20) REVERT: 2 29 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8587 (mttm) REVERT: 2 150 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8550 (mt-10) REVERT: 2 153 ASP cc_start: 0.8729 (m-30) cc_final: 0.8518 (m-30) REVERT: 2 191 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 156 THR cc_start: 0.9421 (m) cc_final: 0.9157 (p) REVERT: A 191 THR cc_start: 0.9342 (m) cc_final: 0.8938 (m) REVERT: A 221 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 232 PHE cc_start: 0.8384 (m-80) cc_final: 0.7783 (m-80) REVERT: H 55 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8752 (mm) REVERT: H 58 TYR cc_start: 0.8693 (t80) cc_final: 0.8381 (t80) REVERT: H 62 GLU cc_start: 0.8718 (tp30) cc_final: 0.8474 (tp30) REVERT: H 139 GLU cc_start: 0.8448 (tp30) cc_final: 0.8004 (tp30) REVERT: H 146 MET cc_start: 0.8747 (mtp) cc_final: 0.8524 (mtp) REVERT: H 153 ASP cc_start: 0.8604 (m-30) cc_final: 0.8195 (m-30) REVERT: O 136 LEU cc_start: 0.9360 (mp) cc_final: 0.9117 (mp) REVERT: O 221 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7806 (t80) REVERT: O 225 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7748 (p0) REVERT: O 227 GLU cc_start: 0.8276 (pm20) cc_final: 0.7958 (pm20) REVERT: V 17 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: V 62 GLU cc_start: 0.8782 (tp30) cc_final: 0.8523 (mm-30) REVERT: V 139 GLU cc_start: 0.8658 (tp30) cc_final: 0.8292 (mm-30) REVERT: V 181 LYS cc_start: 0.8821 (ptpp) cc_final: 0.8610 (ptmm) REVERT: V 186 GLN cc_start: 0.8567 (tp40) cc_final: 0.8321 (tp-100) REVERT: V 193 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 221 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7214 (t80) REVERT: B 232 PHE cc_start: 0.8177 (m-80) cc_final: 0.7919 (m-80) REVERT: I 17 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8385 (pp20) REVERT: I 96 MET cc_start: 0.8858 (mpp) cc_final: 0.8383 (mpp) REVERT: I 191 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7141 (tm-30) REVERT: P 68 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8644 (mm-40) REVERT: P 221 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.5598 (t80) REVERT: P 225 ASP cc_start: 0.8052 (t0) cc_final: 0.7206 (t0) REVERT: P 227 GLU cc_start: 0.8190 (pm20) cc_final: 0.7892 (pm20) REVERT: W 58 TYR cc_start: 0.8834 (t80) cc_final: 0.8471 (t80) REVERT: W 91 LYS cc_start: 0.7960 (pttm) cc_final: 0.7612 (pttp) REVERT: W 173 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9114 (mt) REVERT: W 185 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9012 (m) REVERT: C 191 THR cc_start: 0.9260 (m) cc_final: 0.8977 (p) REVERT: C 221 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.6905 (t80) REVERT: C 225 ASP cc_start: 0.8177 (t70) cc_final: 0.7562 (t70) REVERT: C 227 GLU cc_start: 0.8483 (pm20) cc_final: 0.7900 (pm20) REVERT: C 232 PHE cc_start: 0.8036 (m-80) cc_final: 0.7426 (m-80) REVERT: J 17 GLU cc_start: 0.8699 (pm20) cc_final: 0.8434 (pm20) REVERT: J 58 TYR cc_start: 0.8808 (t80) cc_final: 0.8490 (t80) REVERT: J 93 MET cc_start: 0.8440 (mmt) cc_final: 0.8188 (mmm) REVERT: J 193 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7795 (mt-10) REVERT: Q 118 ASP cc_start: 0.8957 (m-30) cc_final: 0.8555 (m-30) REVERT: Q 156 THR cc_start: 0.9345 (m) cc_final: 0.9089 (p) REVERT: Q 186 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: Q 221 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7271 (t80) REVERT: Q 232 PHE cc_start: 0.8181 (m-80) cc_final: 0.7976 (m-80) REVERT: X 8 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8841 (pp) REVERT: X 17 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: K 17 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: K 150 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8555 (mt-10) REVERT: K 191 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7466 (tm-30) REVERT: R 156 THR cc_start: 0.9427 (m) cc_final: 0.9166 (p) REVERT: R 191 THR cc_start: 0.9354 (m) cc_final: 0.8950 (m) REVERT: R 221 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7384 (t80) REVERT: R 232 PHE cc_start: 0.8381 (m-80) cc_final: 0.7774 (m-80) REVERT: Y 55 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8751 (mm) REVERT: Y 58 TYR cc_start: 0.8683 (t80) cc_final: 0.8335 (t80) REVERT: Y 62 GLU cc_start: 0.8730 (tp30) cc_final: 0.8447 (tp30) REVERT: Y 139 GLU cc_start: 0.8471 (tp30) cc_final: 0.7992 (tp30) REVERT: Y 146 MET cc_start: 0.8767 (mtp) cc_final: 0.8549 (mtp) REVERT: Y 153 ASP cc_start: 0.8612 (m-30) cc_final: 0.8201 (m-30) REVERT: E 136 LEU cc_start: 0.9360 (mp) cc_final: 0.9109 (mp) REVERT: E 221 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.7812 (t80) REVERT: E 225 ASP cc_start: 0.7873 (t70) cc_final: 0.7471 (t70) REVERT: E 227 GLU cc_start: 0.8361 (pm20) cc_final: 0.8048 (pm20) REVERT: L 17 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: L 62 GLU cc_start: 0.8773 (tp30) cc_final: 0.8517 (mm-30) REVERT: L 139 GLU cc_start: 0.8660 (tp30) cc_final: 0.8176 (tp30) REVERT: L 181 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8611 (ptmm) REVERT: L 186 GLN cc_start: 0.8567 (tp40) cc_final: 0.8320 (tp-100) REVERT: L 191 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7707 (tt0) REVERT: L 193 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7750 (mt-10) outliers start: 333 outliers final: 206 residues processed: 1461 average time/residue: 0.2277 time to fit residues: 563.4368 Evaluate side-chains 1321 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1083 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 149 ASP Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 204 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 409 optimal weight: 5.9990 chunk 569 optimal weight: 6.9990 chunk 366 optimal weight: 0.7980 chunk 342 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 310 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 399 optimal weight: 10.0000 chunk 420 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 111 ASN F 62 ASN T 98 GLN T 111 ASN 1 186 GLN G 98 GLN G 122 GLN N 141 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN H 191 GLN ** O 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN P 62 ASN C 98 GLN C 111 ASN J 186 GLN Q 98 GLN Q 122 GLN X 141 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086120 restraints weight = 70489.524| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.33 r_work: 0.2814 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 46816 Z= 0.126 Angle : 0.648 10.618 63182 Z= 0.351 Chirality : 0.045 0.284 7406 Planarity : 0.004 0.055 8106 Dihedral : 7.327 99.993 6697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.42 % Rotamer: Outliers : 6.02 % Allowed : 23.43 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.11), residues: 5922 helix: 2.38 (0.11), residues: 2380 sheet: -0.20 (0.12), residues: 1330 loop : -2.28 (0.11), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 70 TYR 0.021 0.001 TYR H 95 PHE 0.012 0.001 PHE G 42 HIS 0.007 0.003 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00286 (46816) covalent geometry : angle 0.64762 (63182) hydrogen bonds : bond 0.03058 ( 2733) hydrogen bonds : angle 4.73030 ( 7821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 1184 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 136 LEU cc_start: 0.9271 (mt) cc_final: 0.9060 (mt) REVERT: S 221 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.7168 (t80) REVERT: Z 17 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8380 (pp20) REVERT: Z 93 MET cc_start: 0.8614 (mmt) cc_final: 0.8299 (mmm) REVERT: Z 96 MET cc_start: 0.8860 (mpp) cc_final: 0.8385 (mpp) REVERT: Z 191 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7036 (tm-30) REVERT: F 61 GLN cc_start: 0.7885 (pp30) cc_final: 0.7384 (tt0) REVERT: F 68 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8682 (mm-40) REVERT: F 98 GLN cc_start: 0.8688 (tt0) cc_final: 0.8394 (tt0) REVERT: F 221 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.5562 (t80) REVERT: F 225 ASP cc_start: 0.8157 (t70) cc_final: 0.7285 (t70) REVERT: F 226 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8764 (mm110) REVERT: F 227 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: M 58 TYR cc_start: 0.8764 (t80) cc_final: 0.8496 (t80) REVERT: M 93 MET cc_start: 0.8666 (mmt) cc_final: 0.8372 (mmm) REVERT: M 185 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9024 (m) REVERT: M 191 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7606 (tm-30) REVERT: T 44 ASN cc_start: 0.8711 (m-40) cc_final: 0.8495 (m110) REVERT: T 61 GLN cc_start: 0.8251 (mt0) cc_final: 0.8013 (tt0) REVERT: T 221 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7035 (t80) REVERT: T 225 ASP cc_start: 0.8191 (t70) cc_final: 0.7627 (t70) REVERT: T 227 GLU cc_start: 0.8478 (pm20) cc_final: 0.8007 (pm20) REVERT: 1 17 GLU cc_start: 0.8521 (pm20) cc_final: 0.8251 (pm20) REVERT: 1 26 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8603 (pp) REVERT: 1 191 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7633 (tm-30) REVERT: 1 193 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7848 (mt-10) REVERT: G 186 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: G 221 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7310 (t80) REVERT: G 232 PHE cc_start: 0.8310 (m-80) cc_final: 0.8053 (m-80) REVERT: N 17 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: N 139 GLU cc_start: 0.8572 (tp30) cc_final: 0.8146 (tp30) REVERT: N 191 GLN cc_start: 0.7405 (tm-30) cc_final: 0.6674 (tm-30) REVERT: 2 17 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: 2 29 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8803 (mttm) REVERT: 2 146 MET cc_start: 0.8895 (mtp) cc_final: 0.8634 (ptp) REVERT: 2 191 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 61 GLN cc_start: 0.8305 (mt0) cc_final: 0.8074 (tt0) REVERT: A 99 GLU cc_start: 0.8562 (tt0) cc_final: 0.8342 (tt0) REVERT: A 156 THR cc_start: 0.9395 (m) cc_final: 0.9168 (p) REVERT: A 191 THR cc_start: 0.9351 (m) cc_final: 0.8931 (m) REVERT: A 221 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.7480 (t80) REVERT: A 232 PHE cc_start: 0.8400 (m-80) cc_final: 0.7952 (m-80) REVERT: H 55 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8757 (mm) REVERT: H 58 TYR cc_start: 0.8723 (t80) cc_final: 0.8386 (t80) REVERT: H 62 GLU cc_start: 0.8712 (tp30) cc_final: 0.8462 (tp30) REVERT: H 139 GLU cc_start: 0.8599 (tp30) cc_final: 0.8132 (tp30) REVERT: H 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8423 (m-30) REVERT: O 13 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8493 (p) REVERT: O 137 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8945 (mt) REVERT: O 221 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7743 (t80) REVERT: O 225 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7742 (p0) REVERT: O 227 GLU cc_start: 0.8245 (pm20) cc_final: 0.7868 (pm20) REVERT: V 17 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: V 26 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8478 (pp) REVERT: V 139 GLU cc_start: 0.8681 (tp30) cc_final: 0.8260 (tp30) REVERT: V 144 GLU cc_start: 0.8607 (pm20) cc_final: 0.8209 (pm20) REVERT: V 145 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8587 (mmtp) REVERT: V 181 LYS cc_start: 0.8843 (ptpp) cc_final: 0.8622 (ptmm) REVERT: V 193 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 136 LEU cc_start: 0.9282 (mt) cc_final: 0.9067 (mt) REVERT: B 221 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7180 (t80) REVERT: I 17 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8417 (pp20) REVERT: I 93 MET cc_start: 0.8600 (mmt) cc_final: 0.8276 (mmm) REVERT: I 96 MET cc_start: 0.8865 (mpp) cc_final: 0.8398 (mpp) REVERT: I 191 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7024 (tm-30) REVERT: P 61 GLN cc_start: 0.7883 (pp30) cc_final: 0.7386 (tt0) REVERT: P 68 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: P 221 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.5556 (t80) REVERT: P 225 ASP cc_start: 0.8132 (t70) cc_final: 0.7244 (t70) REVERT: P 226 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8754 (mm110) REVERT: P 227 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: W 58 TYR cc_start: 0.8765 (t80) cc_final: 0.8476 (t80) REVERT: W 93 MET cc_start: 0.8571 (mmm) cc_final: 0.8244 (mmm) REVERT: W 185 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9026 (m) REVERT: W 191 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 191 THR cc_start: 0.9265 (m) cc_final: 0.8957 (p) REVERT: C 221 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7049 (t80) REVERT: C 225 ASP cc_start: 0.8225 (t70) cc_final: 0.7664 (t70) REVERT: C 227 GLU cc_start: 0.8515 (pm20) cc_final: 0.8057 (pm20) REVERT: C 232 PHE cc_start: 0.8209 (m-80) cc_final: 0.7771 (m-80) REVERT: J 17 GLU cc_start: 0.8545 (pm20) cc_final: 0.8265 (pm20) REVERT: J 26 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8605 (pp) REVERT: J 191 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7618 (tm-30) REVERT: J 193 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7839 (mt-10) REVERT: Q 156 THR cc_start: 0.9338 (m) cc_final: 0.9131 (p) REVERT: Q 186 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: Q 221 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7297 (t80) REVERT: Q 232 PHE cc_start: 0.8285 (m-80) cc_final: 0.7984 (m-80) REVERT: X 17 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: X 139 GLU cc_start: 0.8553 (tp30) cc_final: 0.8113 (tp30) REVERT: X 191 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6743 (tm-30) REVERT: D 90 ASP cc_start: 0.8488 (m-30) cc_final: 0.8234 (m-30) REVERT: K 17 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: K 29 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8709 (mttm) REVERT: K 146 MET cc_start: 0.8877 (mtp) cc_final: 0.8618 (ptp) REVERT: K 191 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7428 (tm-30) REVERT: R 61 GLN cc_start: 0.8314 (mt0) cc_final: 0.8064 (tt0) REVERT: R 99 GLU cc_start: 0.8574 (tt0) cc_final: 0.8346 (tt0) REVERT: R 156 THR cc_start: 0.9397 (m) cc_final: 0.9172 (p) REVERT: R 191 THR cc_start: 0.9351 (m) cc_final: 0.8922 (m) REVERT: R 221 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7476 (t80) REVERT: R 232 PHE cc_start: 0.8401 (m-80) cc_final: 0.7797 (m-80) REVERT: Y 55 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8748 (mm) REVERT: Y 58 TYR cc_start: 0.8703 (t80) cc_final: 0.8371 (t80) REVERT: Y 62 GLU cc_start: 0.8716 (tp30) cc_final: 0.8462 (tp30) REVERT: Y 139 GLU cc_start: 0.8528 (tp30) cc_final: 0.8078 (tp30) REVERT: E 13 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8506 (p) REVERT: E 137 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8940 (mt) REVERT: E 221 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7741 (t80) REVERT: E 225 ASP cc_start: 0.7897 (t70) cc_final: 0.7494 (t70) REVERT: E 227 GLU cc_start: 0.8288 (pm20) cc_final: 0.7997 (pm20) REVERT: L 17 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: L 26 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8471 (pp) REVERT: L 139 GLU cc_start: 0.8687 (tp30) cc_final: 0.8450 (mm-30) REVERT: L 144 GLU cc_start: 0.8599 (pm20) cc_final: 0.8197 (pm20) REVERT: L 145 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8594 (mmtp) REVERT: L 181 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8609 (ptmm) REVERT: L 191 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7629 (tt0) REVERT: L 193 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7727 (mt-10) outliers start: 300 outliers final: 201 residues processed: 1381 average time/residue: 0.2256 time to fit residues: 526.4034 Evaluate side-chains 1355 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 1115 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 176 LEU Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 149 ASP Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 435 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 445 optimal weight: 0.3980 chunk 262 optimal weight: 5.9990 chunk 502 optimal weight: 0.6980 chunk 492 optimal weight: 2.9990 chunk 364 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 459 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 572 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 23 GLN ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 186 GLN T 23 GLN T 98 GLN T 111 ASN G 98 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 111 ASN H 30 ASN H 191 GLN O 23 GLN B 23 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN C 23 GLN C 111 ASN Q 98 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN R 98 GLN R 111 ASN Y 191 GLN E 23 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083163 restraints weight = 70386.443| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.33 r_work: 0.2755 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46816 Z= 0.179 Angle : 0.675 11.192 63182 Z= 0.364 Chirality : 0.046 0.278 7406 Planarity : 0.004 0.054 8106 Dihedral : 7.276 99.214 6693 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.16 % Favored : 96.59 % Rotamer: Outliers : 6.24 % Allowed : 23.09 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.11), residues: 5922 helix: 2.27 (0.11), residues: 2380 sheet: -0.38 (0.12), residues: 1372 loop : -2.16 (0.11), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Y 57 TYR 0.020 0.002 TYR I 95 PHE 0.021 0.002 PHE C 42 HIS 0.007 0.003 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00425 (46816) covalent geometry : angle 0.67474 (63182) hydrogen bonds : bond 0.03293 ( 2733) hydrogen bonds : angle 4.76631 ( 7821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 311 poor density : 1158 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7124 (t80) REVERT: Z 17 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8473 (pp20) REVERT: Z 93 MET cc_start: 0.8560 (mmt) cc_final: 0.8263 (mmm) REVERT: Z 96 MET cc_start: 0.8877 (mpp) cc_final: 0.8379 (mpp) REVERT: Z 191 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7053 (tm-30) REVERT: F 61 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: F 68 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8786 (mm-40) REVERT: F 73 TYR cc_start: 0.9049 (m-80) cc_final: 0.8681 (m-80) REVERT: F 221 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.5485 (t80) REVERT: F 225 ASP cc_start: 0.8145 (t70) cc_final: 0.7425 (t70) REVERT: F 227 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: F 232 PHE cc_start: 0.7973 (m-80) cc_final: 0.7750 (m-80) REVERT: M 58 TYR cc_start: 0.8779 (t80) cc_final: 0.8497 (t80) REVERT: M 93 MET cc_start: 0.8642 (mmt) cc_final: 0.8396 (mmm) REVERT: M 185 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9046 (m) REVERT: M 191 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7551 (tm-30) REVERT: T 40 MET cc_start: 0.9214 (ttp) cc_final: 0.8999 (ttp) REVERT: T 61 GLN cc_start: 0.8332 (mt0) cc_final: 0.8078 (tt0) REVERT: T 221 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7087 (t80) REVERT: T 225 ASP cc_start: 0.8272 (t70) cc_final: 0.7696 (t70) REVERT: T 227 GLU cc_start: 0.8473 (pm20) cc_final: 0.8067 (pm20) REVERT: 1 17 GLU cc_start: 0.8553 (pm20) cc_final: 0.8259 (pm20) REVERT: 1 26 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8709 (pp) REVERT: 1 191 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7532 (tm-30) REVERT: 1 193 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 221 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7318 (t80) REVERT: N 17 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: N 191 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6890 (tm-30) REVERT: U 61 GLN cc_start: 0.8461 (mt0) cc_final: 0.8192 (tt0) REVERT: U 90 ASP cc_start: 0.8620 (m-30) cc_final: 0.8247 (m-30) REVERT: 2 17 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8335 (pp20) REVERT: 2 29 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8812 (mttm) REVERT: 2 150 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8521 (mt-10) REVERT: 2 191 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 53 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6768 (mmmt) REVERT: A 61 GLN cc_start: 0.8369 (mt0) cc_final: 0.8108 (tt0) REVERT: A 156 THR cc_start: 0.9400 (m) cc_final: 0.9138 (p) REVERT: A 221 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7513 (t80) REVERT: H 51 ASP cc_start: 0.8495 (m-30) cc_final: 0.8107 (m-30) REVERT: H 55 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8777 (mm) REVERT: H 58 TYR cc_start: 0.8721 (t80) cc_final: 0.8355 (t80) REVERT: H 62 GLU cc_start: 0.8772 (tp30) cc_final: 0.8523 (tp30) REVERT: H 139 GLU cc_start: 0.8715 (tp30) cc_final: 0.8295 (tp30) REVERT: H 144 GLU cc_start: 0.8529 (pm20) cc_final: 0.8313 (pm20) REVERT: H 153 ASP cc_start: 0.8671 (m-30) cc_final: 0.8449 (m-30) REVERT: O 13 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8514 (p) REVERT: O 61 GLN cc_start: 0.8092 (tt0) cc_final: 0.7698 (tm-30) REVERT: O 137 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8904 (mt) REVERT: O 221 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7635 (t80) REVERT: O 225 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7756 (p0) REVERT: O 227 GLU cc_start: 0.8145 (pm20) cc_final: 0.7820 (pm20) REVERT: V 9 LYS cc_start: 0.9131 (tppt) cc_final: 0.8915 (tptp) REVERT: V 17 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: V 26 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8632 (pp) REVERT: V 139 GLU cc_start: 0.8862 (tp30) cc_final: 0.8551 (mm-30) REVERT: V 153 ASP cc_start: 0.8863 (m-30) cc_final: 0.8644 (m-30) REVERT: V 181 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8610 (ptmm) REVERT: B 221 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7134 (t80) REVERT: I 17 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8469 (pp20) REVERT: I 93 MET cc_start: 0.8548 (mmt) cc_final: 0.8244 (mmm) REVERT: I 96 MET cc_start: 0.8889 (mpp) cc_final: 0.8391 (mpp) REVERT: I 191 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7043 (tm-30) REVERT: P 61 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: P 68 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8766 (mm-40) REVERT: P 221 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.5469 (t80) REVERT: P 227 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: P 232 PHE cc_start: 0.8007 (m-80) cc_final: 0.7785 (m-80) REVERT: W 58 TYR cc_start: 0.8781 (t80) cc_final: 0.8484 (t80) REVERT: W 185 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9048 (m) REVERT: W 191 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 40 MET cc_start: 0.9213 (ttp) cc_final: 0.8991 (ttp) REVERT: C 191 THR cc_start: 0.9251 (m) cc_final: 0.8969 (p) REVERT: C 221 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 225 ASP cc_start: 0.8262 (t70) cc_final: 0.7574 (t70) REVERT: C 227 GLU cc_start: 0.8462 (pm20) cc_final: 0.8064 (pm20) REVERT: C 232 PHE cc_start: 0.8226 (m-80) cc_final: 0.7777 (m-80) REVERT: J 17 GLU cc_start: 0.8535 (pm20) cc_final: 0.8257 (pm20) REVERT: J 26 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8729 (pp) REVERT: J 191 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7592 (tm-30) REVERT: J 193 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7850 (mt-10) REVERT: Q 118 ASP cc_start: 0.8949 (m-30) cc_final: 0.8637 (m-30) REVERT: Q 156 THR cc_start: 0.9361 (m) cc_final: 0.9155 (p) REVERT: Q 221 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7318 (t80) REVERT: X 17 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: X 191 GLN cc_start: 0.7413 (tm-30) cc_final: 0.6916 (tm-30) REVERT: D 61 GLN cc_start: 0.8473 (mt0) cc_final: 0.8191 (tt0) REVERT: D 90 ASP cc_start: 0.8635 (m-30) cc_final: 0.8252 (m-30) REVERT: K 17 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: K 150 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8518 (mt-10) REVERT: K 191 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7425 (tm-30) REVERT: R 61 GLN cc_start: 0.8335 (mt0) cc_final: 0.8091 (tt0) REVERT: R 99 GLU cc_start: 0.8614 (tt0) cc_final: 0.8330 (tt0) REVERT: R 132 TYR cc_start: 0.9211 (m-80) cc_final: 0.8992 (m-10) REVERT: R 156 THR cc_start: 0.9406 (m) cc_final: 0.9155 (p) REVERT: R 221 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7537 (t80) REVERT: Y 51 ASP cc_start: 0.8477 (m-30) cc_final: 0.8088 (m-30) REVERT: Y 55 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8782 (mm) REVERT: Y 58 TYR cc_start: 0.8734 (t80) cc_final: 0.8372 (t80) REVERT: Y 62 GLU cc_start: 0.8771 (tp30) cc_final: 0.8531 (tp30) REVERT: Y 139 GLU cc_start: 0.8615 (tp30) cc_final: 0.8158 (tp30) REVERT: Y 144 GLU cc_start: 0.8536 (pm20) cc_final: 0.8321 (pm20) REVERT: E 13 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8515 (p) REVERT: E 137 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8894 (mt) REVERT: E 221 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7721 (t80) REVERT: E 225 ASP cc_start: 0.8082 (t70) cc_final: 0.7641 (t70) REVERT: E 227 GLU cc_start: 0.8317 (pm20) cc_final: 0.8077 (pm20) REVERT: L 9 LYS cc_start: 0.9124 (tppt) cc_final: 0.8895 (tptp) REVERT: L 17 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: L 26 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8627 (pp) REVERT: L 181 LYS cc_start: 0.8818 (ptpp) cc_final: 0.8613 (ptmm) REVERT: L 191 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7591 (tt0) outliers start: 311 outliers final: 233 residues processed: 1360 average time/residue: 0.2225 time to fit residues: 511.4369 Evaluate side-chains 1347 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 1074 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 8 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 176 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 333 optimal weight: 5.9990 chunk 429 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 432 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 111 ASN Z 186 GLN T 98 GLN T 111 ASN G 98 GLN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 GLN A 98 GLN A 111 ASN H 30 ASN H 191 GLN B 111 ASN I 186 GLN C 98 GLN C 111 ASN Q 98 GLN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 111 ASN Y 191 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.082903 restraints weight = 70654.083| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.35 r_work: 0.2758 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 46816 Z= 0.173 Angle : 0.685 11.853 63182 Z= 0.369 Chirality : 0.046 0.279 7406 Planarity : 0.004 0.054 8106 Dihedral : 7.243 98.068 6689 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Rotamer: Outliers : 6.26 % Allowed : 23.11 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.11), residues: 5922 helix: 2.31 (0.11), residues: 2394 sheet: -0.33 (0.12), residues: 1372 loop : -2.19 (0.11), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 70 TYR 0.020 0.002 TYR Y 95 PHE 0.026 0.002 PHE G 232 HIS 0.007 0.003 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00408 (46816) covalent geometry : angle 0.68536 (63182) hydrogen bonds : bond 0.03278 ( 2733) hydrogen bonds : angle 4.73766 ( 7821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 1118 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7193 (t80) REVERT: S 232 PHE cc_start: 0.8202 (m-80) cc_final: 0.7473 (t80) REVERT: Z 17 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8436 (pp20) REVERT: Z 191 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7027 (tm-30) REVERT: F 61 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: F 68 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8776 (mm-40) REVERT: F 73 TYR cc_start: 0.9039 (m-80) cc_final: 0.8643 (m-80) REVERT: F 221 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.5506 (t80) REVERT: F 225 ASP cc_start: 0.8164 (t70) cc_final: 0.7374 (t70) REVERT: F 226 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8817 (mm110) REVERT: F 227 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: M 58 TYR cc_start: 0.8806 (t80) cc_final: 0.8519 (t80) REVERT: M 93 MET cc_start: 0.8690 (mmt) cc_final: 0.8423 (mmm) REVERT: M 185 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9083 (m) REVERT: M 191 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7643 (tm-30) REVERT: T 40 MET cc_start: 0.9189 (ttp) cc_final: 0.8916 (ttp) REVERT: T 61 GLN cc_start: 0.8395 (mt0) cc_final: 0.8086 (tt0) REVERT: T 221 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7081 (t80) REVERT: 1 17 GLU cc_start: 0.8557 (pm20) cc_final: 0.8268 (pm20) REVERT: 1 26 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8747 (pp) REVERT: 1 58 TYR cc_start: 0.8923 (t80) cc_final: 0.8649 (t80) REVERT: 1 191 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7385 (tm-30) REVERT: 1 193 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7755 (mt-10) REVERT: G 53 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6568 (mmmt) REVERT: G 221 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7356 (t80) REVERT: N 17 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: N 139 GLU cc_start: 0.8593 (tp30) cc_final: 0.8182 (tp30) REVERT: N 191 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6831 (tm-30) REVERT: U 61 GLN cc_start: 0.8480 (mt0) cc_final: 0.8187 (tt0) REVERT: U 90 ASP cc_start: 0.8633 (m-30) cc_final: 0.8406 (m-30) REVERT: 2 17 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8317 (pp20) REVERT: 2 191 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 53 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6432 (mmmt) REVERT: A 61 GLN cc_start: 0.8419 (mt0) cc_final: 0.8146 (tt0) REVERT: A 156 THR cc_start: 0.9408 (m) cc_final: 0.9155 (p) REVERT: A 221 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 232 PHE cc_start: 0.8200 (m-80) cc_final: 0.7761 (m-80) REVERT: H 51 ASP cc_start: 0.8476 (m-30) cc_final: 0.8081 (m-30) REVERT: H 55 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8747 (mm) REVERT: H 58 TYR cc_start: 0.8713 (t80) cc_final: 0.8363 (t80) REVERT: H 93 MET cc_start: 0.8488 (mmm) cc_final: 0.8204 (mmm) REVERT: H 139 GLU cc_start: 0.8691 (tp30) cc_final: 0.8282 (tp30) REVERT: H 144 GLU cc_start: 0.8616 (pm20) cc_final: 0.8348 (pm20) REVERT: H 153 ASP cc_start: 0.8668 (m-30) cc_final: 0.8439 (m-30) REVERT: O 13 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8517 (p) REVERT: O 137 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8888 (mt) REVERT: O 150 ASP cc_start: 0.8535 (t70) cc_final: 0.8315 (t0) REVERT: O 221 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7644 (t80) REVERT: O 225 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7584 (p0) REVERT: O 227 GLU cc_start: 0.8155 (pm20) cc_final: 0.7790 (pm20) REVERT: V 17 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8242 (pp20) REVERT: V 26 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8650 (pp) REVERT: V 181 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8539 (ptmm) REVERT: V 193 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7643 (mt-10) REVERT: B 221 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 232 PHE cc_start: 0.8208 (m-80) cc_final: 0.7485 (t80) REVERT: I 17 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8424 (pp20) REVERT: I 191 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7023 (tm-30) REVERT: P 61 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: P 68 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8765 (mm-40) REVERT: P 221 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.5461 (t80) REVERT: P 225 ASP cc_start: 0.8149 (t70) cc_final: 0.7439 (t70) REVERT: P 226 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8812 (mm110) REVERT: P 227 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: W 58 TYR cc_start: 0.8794 (t80) cc_final: 0.8514 (t80) REVERT: W 185 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9084 (m) REVERT: W 191 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 40 MET cc_start: 0.9198 (ttp) cc_final: 0.8903 (ttp) REVERT: C 191 THR cc_start: 0.9244 (m) cc_final: 0.8963 (p) REVERT: C 221 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7097 (t80) REVERT: C 225 ASP cc_start: 0.8364 (t70) cc_final: 0.7565 (t70) REVERT: C 227 GLU cc_start: 0.8437 (pm20) cc_final: 0.7853 (pm20) REVERT: C 232 PHE cc_start: 0.8228 (m-80) cc_final: 0.7770 (m-80) REVERT: J 17 GLU cc_start: 0.8561 (pm20) cc_final: 0.8278 (pm20) REVERT: J 26 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8714 (pp) REVERT: J 191 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7482 (tm-30) REVERT: J 193 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7759 (mt-10) REVERT: Q 53 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6566 (mmmt) REVERT: Q 156 THR cc_start: 0.9354 (m) cc_final: 0.9139 (p) REVERT: Q 221 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7347 (t80) REVERT: X 17 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: X 93 MET cc_start: 0.8562 (mmt) cc_final: 0.8352 (mmt) REVERT: X 139 GLU cc_start: 0.8572 (tp30) cc_final: 0.8128 (tp30) REVERT: X 191 GLN cc_start: 0.7485 (tm-30) cc_final: 0.6917 (tm-30) REVERT: D 61 GLN cc_start: 0.8467 (mt0) cc_final: 0.8185 (tt0) REVERT: D 90 ASP cc_start: 0.8648 (m-30) cc_final: 0.8417 (m-30) REVERT: K 17 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8354 (pp20) REVERT: K 191 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7448 (tm-30) REVERT: R 61 GLN cc_start: 0.8427 (mt0) cc_final: 0.8151 (tt0) REVERT: R 136 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9210 (mp) REVERT: R 156 THR cc_start: 0.9393 (m) cc_final: 0.9161 (p) REVERT: R 221 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7521 (t80) REVERT: R 232 PHE cc_start: 0.8191 (m-80) cc_final: 0.7751 (m-80) REVERT: Y 51 ASP cc_start: 0.8469 (m-30) cc_final: 0.8065 (m-30) REVERT: Y 55 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8755 (mm) REVERT: Y 58 TYR cc_start: 0.8720 (t80) cc_final: 0.8373 (t80) REVERT: Y 144 GLU cc_start: 0.8617 (pm20) cc_final: 0.8349 (pm20) REVERT: E 13 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8504 (p) REVERT: E 137 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (mt) REVERT: E 150 ASP cc_start: 0.8536 (t70) cc_final: 0.8318 (t0) REVERT: E 221 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7648 (t80) REVERT: E 225 ASP cc_start: 0.8169 (t70) cc_final: 0.7747 (t70) REVERT: E 227 GLU cc_start: 0.8345 (pm20) cc_final: 0.8085 (pm20) REVERT: L 17 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: L 26 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8643 (pp) REVERT: L 181 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8501 (ptmm) REVERT: L 191 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7561 (tt0) outliers start: 312 outliers final: 238 residues processed: 1316 average time/residue: 0.1896 time to fit residues: 420.5393 Evaluate side-chains 1378 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 1097 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 GLN Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 176 LEU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 149 ASP Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 264 optimal weight: 5.9990 chunk 559 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 503 optimal weight: 8.9990 chunk 555 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 580 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 411 optimal weight: 0.0170 chunk 167 optimal weight: 2.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 98 GLN T 111 ASN G 98 GLN G 111 ASN G 122 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 111 ASN H 30 ASN H 191 GLN O 111 ASN C 111 ASN Q 98 GLN Q 111 ASN Q 122 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 111 ASN Y 191 GLN E 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.084191 restraints weight = 70268.314| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.33 r_work: 0.2780 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 46816 Z= 0.149 Angle : 0.690 12.602 63182 Z= 0.370 Chirality : 0.046 0.275 7406 Planarity : 0.004 0.057 8106 Dihedral : 7.182 96.218 6685 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.48 % Favored : 96.27 % Rotamer: Outliers : 5.96 % Allowed : 23.56 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.11), residues: 5922 helix: 2.33 (0.11), residues: 2408 sheet: -0.30 (0.12), residues: 1372 loop : -2.19 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 70 TYR 0.022 0.001 TYR J 58 PHE 0.027 0.002 PHE P 232 HIS 0.007 0.003 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00353 (46816) covalent geometry : angle 0.69013 (63182) hydrogen bonds : bond 0.03147 ( 2733) hydrogen bonds : angle 4.70733 ( 7821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 1107 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7199 (t80) REVERT: Z 17 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8442 (pp20) REVERT: Z 26 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8762 (pp) REVERT: Z 144 GLU cc_start: 0.8252 (pm20) cc_final: 0.8014 (pm20) REVERT: Z 186 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: Z 191 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7045 (tm-30) REVERT: F 61 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: F 73 TYR cc_start: 0.9021 (m-80) cc_final: 0.8587 (m-80) REVERT: F 221 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.5558 (t80) REVERT: F 225 ASP cc_start: 0.8133 (t70) cc_final: 0.7439 (t70) REVERT: F 226 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8805 (mm110) REVERT: F 227 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: M 58 TYR cc_start: 0.8796 (t80) cc_final: 0.8524 (t80) REVERT: M 93 MET cc_start: 0.8759 (mmt) cc_final: 0.8507 (mmm) REVERT: M 185 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9102 (m) REVERT: T 40 MET cc_start: 0.9154 (ttp) cc_final: 0.8842 (ttp) REVERT: T 61 GLN cc_start: 0.8364 (mt0) cc_final: 0.8077 (tt0) REVERT: T 221 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.7097 (t80) REVERT: T 232 PHE cc_start: 0.7947 (m-80) cc_final: 0.7580 (t80) REVERT: 1 17 GLU cc_start: 0.8395 (pm20) cc_final: 0.8156 (pm20) REVERT: 1 26 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8688 (pp) REVERT: 1 93 MET cc_start: 0.8580 (mmt) cc_final: 0.8329 (mmm) REVERT: 1 191 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7370 (tm-30) REVERT: 1 193 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7790 (mt-10) REVERT: G 61 GLN cc_start: 0.8143 (tt0) cc_final: 0.7710 (tm-30) REVERT: G 221 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7332 (t80) REVERT: G 232 PHE cc_start: 0.8297 (m-80) cc_final: 0.7736 (t80) REVERT: N 17 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: N 139 GLU cc_start: 0.8562 (tp30) cc_final: 0.8188 (tp30) REVERT: N 191 GLN cc_start: 0.7450 (tm-30) cc_final: 0.6825 (tm-30) REVERT: U 61 GLN cc_start: 0.8446 (mt0) cc_final: 0.8191 (tt0) REVERT: U 90 ASP cc_start: 0.8615 (m-30) cc_final: 0.8238 (m-30) REVERT: 2 17 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8226 (pp20) REVERT: 2 146 MET cc_start: 0.8954 (mtp) cc_final: 0.8748 (ptp) REVERT: 2 191 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 53 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6290 (mmmt) REVERT: A 61 GLN cc_start: 0.8407 (mt0) cc_final: 0.8142 (tt0) REVERT: A 156 THR cc_start: 0.9390 (m) cc_final: 0.9148 (p) REVERT: A 221 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 232 PHE cc_start: 0.8234 (m-80) cc_final: 0.8019 (m-80) REVERT: H 55 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8738 (mm) REVERT: H 58 TYR cc_start: 0.8716 (t80) cc_final: 0.8336 (t80) REVERT: H 62 GLU cc_start: 0.8793 (tp30) cc_final: 0.8541 (tp30) REVERT: H 144 GLU cc_start: 0.8591 (pm20) cc_final: 0.8237 (pm20) REVERT: H 146 MET cc_start: 0.8756 (mtp) cc_final: 0.8530 (mtp) REVERT: H 153 ASP cc_start: 0.8667 (m-30) cc_final: 0.8432 (m-30) REVERT: O 13 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8478 (p) REVERT: O 61 GLN cc_start: 0.7991 (tt0) cc_final: 0.7606 (tm-30) REVERT: O 137 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8867 (mt) REVERT: O 150 ASP cc_start: 0.8448 (t70) cc_final: 0.8233 (t0) REVERT: O 221 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7702 (t80) REVERT: O 225 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7552 (p0) REVERT: O 227 GLU cc_start: 0.8135 (pm20) cc_final: 0.7775 (pm20) REVERT: V 17 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8201 (pp20) REVERT: V 26 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8629 (pp) REVERT: V 139 GLU cc_start: 0.8789 (tp30) cc_final: 0.8406 (mm-30) REVERT: V 181 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8482 (ptmm) REVERT: B 221 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7188 (t80) REVERT: I 17 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: I 26 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8755 (pp) REVERT: I 144 GLU cc_start: 0.8292 (pm20) cc_final: 0.8043 (pm20) REVERT: I 186 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: I 191 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7048 (tm-30) REVERT: P 61 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: P 68 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8722 (mm-40) REVERT: P 221 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.5542 (t80) REVERT: P 225 ASP cc_start: 0.8136 (t70) cc_final: 0.7349 (t70) REVERT: P 226 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8797 (mm110) REVERT: P 227 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: W 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8539 (t80) REVERT: W 93 MET cc_start: 0.8604 (mmm) cc_final: 0.8315 (mmm) REVERT: W 185 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9097 (m) REVERT: C 40 MET cc_start: 0.9144 (ttp) cc_final: 0.8894 (ttp) REVERT: C 61 GLN cc_start: 0.7944 (pm20) cc_final: 0.7520 (pp30) REVERT: C 191 THR cc_start: 0.9233 (m) cc_final: 0.8962 (p) REVERT: C 221 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7096 (t80) REVERT: C 225 ASP cc_start: 0.8305 (t70) cc_final: 0.7652 (t70) REVERT: C 227 GLU cc_start: 0.8404 (pm20) cc_final: 0.8021 (pm20) REVERT: C 232 PHE cc_start: 0.8250 (m-80) cc_final: 0.7935 (m-80) REVERT: J 17 GLU cc_start: 0.8378 (pm20) cc_final: 0.8126 (pm20) REVERT: J 26 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8688 (pp) REVERT: J 93 MET cc_start: 0.8558 (mmt) cc_final: 0.8266 (mmm) REVERT: J 191 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7491 (tm-30) REVERT: J 193 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7804 (mt-10) REVERT: Q 61 GLN cc_start: 0.8153 (tt0) cc_final: 0.7714 (tm-30) REVERT: Q 118 ASP cc_start: 0.8908 (m-30) cc_final: 0.8606 (m-30) REVERT: Q 221 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.7338 (t80) REVERT: Q 232 PHE cc_start: 0.8293 (m-80) cc_final: 0.7654 (t80) REVERT: X 17 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: X 93 MET cc_start: 0.8551 (mmt) cc_final: 0.8328 (mmt) REVERT: X 139 GLU cc_start: 0.8567 (tp30) cc_final: 0.8202 (tp30) REVERT: X 191 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6865 (tm-30) REVERT: D 61 GLN cc_start: 0.8458 (mt0) cc_final: 0.8194 (tt0) REVERT: D 90 ASP cc_start: 0.8621 (m-30) cc_final: 0.8395 (m-30) REVERT: K 17 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8202 (pp20) REVERT: K 146 MET cc_start: 0.8925 (mtp) cc_final: 0.8710 (ptp) REVERT: K 191 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7448 (tm-30) REVERT: R 61 GLN cc_start: 0.8430 (mt0) cc_final: 0.8149 (tt0) REVERT: R 99 GLU cc_start: 0.8723 (tt0) cc_final: 0.8522 (tt0) REVERT: R 136 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9216 (mp) REVERT: R 156 THR cc_start: 0.9394 (m) cc_final: 0.9188 (p) REVERT: R 221 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7572 (t80) REVERT: R 232 PHE cc_start: 0.8226 (m-80) cc_final: 0.8002 (m-80) REVERT: Y 58 TYR cc_start: 0.8711 (t80) cc_final: 0.8360 (t80) REVERT: Y 139 GLU cc_start: 0.8622 (tp30) cc_final: 0.8321 (mm-30) REVERT: Y 144 GLU cc_start: 0.8619 (pm20) cc_final: 0.8250 (pm20) REVERT: Y 146 MET cc_start: 0.8783 (mtp) cc_final: 0.8556 (mtp) REVERT: E 13 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8490 (p) REVERT: E 61 GLN cc_start: 0.8009 (tt0) cc_final: 0.7614 (tm-30) REVERT: E 137 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8861 (mt) REVERT: E 221 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7714 (t80) REVERT: L 17 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: L 26 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8624 (pp) REVERT: L 181 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8522 (ptmm) REVERT: L 191 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7574 (tt0) outliers start: 297 outliers final: 221 residues processed: 1288 average time/residue: 0.1717 time to fit residues: 373.5211 Evaluate side-chains 1309 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 1045 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 112 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 186 GLN Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 227 GLU Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 186 GLN Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 51 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 532 optimal weight: 0.7980 chunk 296 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 479 optimal weight: 8.9990 chunk 514 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 ASN M 30 ASN T 122 GLN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 ASN A 98 GLN A 111 ASN H 30 ASN H 191 GLN O 111 ASN P 111 ASN W 30 ASN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN R 98 GLN R 111 ASN R 219 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN E 111 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085153 restraints weight = 70495.690| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.33 r_work: 0.2796 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46816 Z= 0.143 Angle : 0.695 13.083 63182 Z= 0.371 Chirality : 0.046 0.256 7406 Planarity : 0.004 0.056 8106 Dihedral : 7.083 94.626 6679 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.68 % Favored : 96.07 % Rotamer: Outliers : 5.42 % Allowed : 24.44 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.11), residues: 5922 helix: 2.40 (0.11), residues: 2394 sheet: -0.31 (0.12), residues: 1372 loop : -2.18 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 70 TYR 0.030 0.001 TYR J 58 PHE 0.021 0.002 PHE C 42 HIS 0.007 0.003 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00334 (46816) covalent geometry : angle 0.69501 (63182) hydrogen bonds : bond 0.03069 ( 2733) hydrogen bonds : angle 4.67421 ( 7821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11844 Ramachandran restraints generated. 5922 Oldfield, 0 Emsley, 5922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 1101 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 221 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7210 (t80) REVERT: S 232 PHE cc_start: 0.8011 (m-80) cc_final: 0.7728 (t80) REVERT: Z 17 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: Z 26 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8738 (pp) REVERT: Z 58 TYR cc_start: 0.8846 (t80) cc_final: 0.8592 (t80) REVERT: Z 93 MET cc_start: 0.8387 (mmm) cc_final: 0.7661 (ptp) REVERT: Z 95 TYR cc_start: 0.8710 (m-80) cc_final: 0.8431 (m-10) REVERT: Z 144 GLU cc_start: 0.8244 (pm20) cc_final: 0.7992 (pm20) REVERT: Z 191 GLN cc_start: 0.7538 (tm-30) cc_final: 0.6957 (tm-30) REVERT: F 61 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: F 73 TYR cc_start: 0.9019 (m-80) cc_final: 0.8629 (m-80) REVERT: F 114 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8646 (mtmt) REVERT: F 221 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.5522 (t80) REVERT: F 225 ASP cc_start: 0.8208 (t70) cc_final: 0.7467 (t70) REVERT: F 226 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8804 (mm110) REVERT: F 227 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: F 232 PHE cc_start: 0.8019 (m-80) cc_final: 0.7275 (t80) REVERT: M 58 TYR cc_start: 0.8792 (t80) cc_final: 0.8528 (t80) REVERT: M 93 MET cc_start: 0.8752 (mmt) cc_final: 0.8539 (mmm) REVERT: M 191 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7488 (tm-30) REVERT: T 40 MET cc_start: 0.9166 (ttp) cc_final: 0.8867 (ttp) REVERT: T 221 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.7062 (t80) REVERT: T 232 PHE cc_start: 0.7839 (m-80) cc_final: 0.7083 (t80) REVERT: 1 17 GLU cc_start: 0.8289 (pm20) cc_final: 0.8057 (pm20) REVERT: 1 26 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8675 (pp) REVERT: 1 93 MET cc_start: 0.8540 (mmt) cc_final: 0.8293 (mmm) REVERT: 1 191 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7333 (tm-30) REVERT: 1 193 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7774 (mt-10) REVERT: G 61 GLN cc_start: 0.8232 (tt0) cc_final: 0.7916 (tm-30) REVERT: G 221 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7361 (t80) REVERT: G 232 PHE cc_start: 0.8240 (m-80) cc_final: 0.7404 (t80) REVERT: N 17 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: N 58 TYR cc_start: 0.8919 (t80) cc_final: 0.8555 (t80) REVERT: N 93 MET cc_start: 0.8540 (mmt) cc_final: 0.8119 (mmm) REVERT: N 139 GLU cc_start: 0.8554 (tp30) cc_final: 0.8185 (tp30) REVERT: N 191 GLN cc_start: 0.7463 (tm-30) cc_final: 0.6779 (tm-30) REVERT: U 61 GLN cc_start: 0.8483 (mt0) cc_final: 0.8194 (tt0) REVERT: U 90 ASP cc_start: 0.8505 (m-30) cc_final: 0.8128 (m-30) REVERT: 2 17 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: 2 185 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9194 (m) REVERT: 2 191 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 53 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6331 (mmmt) REVERT: A 61 GLN cc_start: 0.8430 (mt0) cc_final: 0.8157 (tt0) REVERT: A 156 THR cc_start: 0.9427 (m) cc_final: 0.9195 (p) REVERT: A 221 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7563 (t80) REVERT: H 58 TYR cc_start: 0.8728 (t80) cc_final: 0.8335 (t80) REVERT: H 62 GLU cc_start: 0.8801 (tp30) cc_final: 0.8560 (tp30) REVERT: H 139 GLU cc_start: 0.8636 (tp30) cc_final: 0.8141 (mm-30) REVERT: H 144 GLU cc_start: 0.8458 (pm20) cc_final: 0.8082 (pm20) REVERT: H 146 MET cc_start: 0.8711 (mtp) cc_final: 0.8472 (mtp) REVERT: H 153 ASP cc_start: 0.8696 (m-30) cc_final: 0.8454 (m-30) REVERT: O 13 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8444 (p) REVERT: O 61 GLN cc_start: 0.8011 (tt0) cc_final: 0.7599 (tm-30) REVERT: O 137 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8846 (mt) REVERT: O 221 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.7709 (t80) REVERT: O 225 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7534 (p0) REVERT: O 227 GLU cc_start: 0.8211 (pm20) cc_final: 0.7800 (pm20) REVERT: V 17 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: V 26 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8615 (pp) REVERT: V 139 GLU cc_start: 0.8802 (tp30) cc_final: 0.8520 (mm-30) REVERT: V 150 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8537 (mt-10) REVERT: V 181 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8469 (ptmm) REVERT: B 221 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7205 (t80) REVERT: B 232 PHE cc_start: 0.8014 (m-80) cc_final: 0.7731 (t80) REVERT: I 17 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8421 (pp20) REVERT: I 26 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8738 (pp) REVERT: I 58 TYR cc_start: 0.8860 (t80) cc_final: 0.8604 (t80) REVERT: I 93 MET cc_start: 0.8422 (mmm) cc_final: 0.7674 (ptp) REVERT: I 95 TYR cc_start: 0.8711 (m-80) cc_final: 0.8428 (m-10) REVERT: I 144 GLU cc_start: 0.8243 (pm20) cc_final: 0.7994 (pm20) REVERT: I 191 GLN cc_start: 0.7522 (tm-30) cc_final: 0.6943 (tm-30) REVERT: P 61 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: P 114 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8664 (mtmt) REVERT: P 221 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.5532 (t80) REVERT: P 225 ASP cc_start: 0.8215 (t70) cc_final: 0.7468 (t70) REVERT: P 226 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8806 (mm110) REVERT: P 227 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: P 232 PHE cc_start: 0.8088 (m-80) cc_final: 0.7359 (t80) REVERT: W 58 TYR cc_start: 0.8818 (t80) cc_final: 0.8542 (t80) REVERT: W 93 MET cc_start: 0.8625 (mmm) cc_final: 0.8299 (mmm) REVERT: W 191 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 40 MET cc_start: 0.9155 (ttp) cc_final: 0.8927 (ttp) REVERT: C 61 GLN cc_start: 0.7927 (pm20) cc_final: 0.7564 (pp30) REVERT: C 191 THR cc_start: 0.9254 (m) cc_final: 0.8975 (p) REVERT: C 221 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7022 (t80) REVERT: C 225 ASP cc_start: 0.8340 (t70) cc_final: 0.7675 (t70) REVERT: C 227 GLU cc_start: 0.8311 (pm20) cc_final: 0.7952 (pm20) REVERT: C 232 PHE cc_start: 0.8240 (m-80) cc_final: 0.7931 (m-80) REVERT: J 17 GLU cc_start: 0.8277 (pm20) cc_final: 0.8040 (pm20) REVERT: J 26 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8673 (pp) REVERT: J 93 MET cc_start: 0.8547 (mmt) cc_final: 0.8309 (mmm) REVERT: J 191 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7461 (tm-30) REVERT: J 193 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7774 (mt-10) REVERT: Q 61 GLN cc_start: 0.8230 (tt0) cc_final: 0.7910 (tm-30) REVERT: Q 221 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7342 (t80) REVERT: Q 232 PHE cc_start: 0.8252 (m-80) cc_final: 0.7342 (t80) REVERT: X 17 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: X 93 MET cc_start: 0.8527 (mmt) cc_final: 0.8293 (mmt) REVERT: X 139 GLU cc_start: 0.8553 (tp30) cc_final: 0.8140 (tp30) REVERT: X 191 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6773 (tm-30) REVERT: D 61 GLN cc_start: 0.8487 (mt0) cc_final: 0.8202 (tt0) REVERT: D 90 ASP cc_start: 0.8509 (m-30) cc_final: 0.8127 (m-30) REVERT: K 17 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: K 185 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9176 (m) REVERT: K 191 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7474 (tm-30) REVERT: R 61 GLN cc_start: 0.8486 (mt0) cc_final: 0.8177 (tt0) REVERT: R 99 GLU cc_start: 0.8684 (tt0) cc_final: 0.8477 (tt0) REVERT: R 221 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7423 (t80) REVERT: Y 58 TYR cc_start: 0.8725 (t80) cc_final: 0.8325 (t80) REVERT: Y 62 GLU cc_start: 0.8808 (tp30) cc_final: 0.8563 (tp30) REVERT: Y 139 GLU cc_start: 0.8602 (tp30) cc_final: 0.8177 (tp30) REVERT: Y 144 GLU cc_start: 0.8422 (pm20) cc_final: 0.8044 (pm20) REVERT: E 13 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8452 (p) REVERT: E 61 GLN cc_start: 0.8028 (tt0) cc_final: 0.7605 (tm-30) REVERT: E 137 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8856 (mt) REVERT: E 150 ASP cc_start: 0.8478 (t70) cc_final: 0.8251 (t0) REVERT: E 221 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7808 (t80) REVERT: E 225 ASP cc_start: 0.8008 (t70) cc_final: 0.7709 (t70) REVERT: L 17 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8220 (pp20) REVERT: L 26 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8607 (pp) REVERT: L 139 GLU cc_start: 0.8775 (tp30) cc_final: 0.8448 (mm-30) REVERT: L 181 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8523 (ptmm) REVERT: L 191 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7546 (tt0) outliers start: 270 outliers final: 207 residues processed: 1260 average time/residue: 0.1683 time to fit residues: 357.3473 Evaluate side-chains 1320 residues out of total 4984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 1075 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain T residue 13 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 227 GLU Chi-restraints excluded: chain 1 residue 8 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 134 VAL Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 47 LEU Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 59 MET Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 165 ARG Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 225 ASP Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 60 LYS Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 86 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 59 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 40 MET Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain P residue 216 THR Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 124 THR Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 172 MET Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain R residue 225 ASP Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 121 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 123 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 478 optimal weight: 5.9990 chunk 498 optimal weight: 3.9990 chunk 557 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 418 optimal weight: 7.9990 chunk 482 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN F 226 GLN ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 ASN T 122 GLN G 23 GLN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 111 ASN A 219 ASN O 111 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 GLN P 226 GLN W 30 ASN C 111 ASN Q 23 GLN ** X 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 111 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.079894 restraints weight = 70705.146| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.31 r_work: 0.2699 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 46816 Z= 0.310 Angle : 0.798 12.775 63182 Z= 0.425 Chirality : 0.050 0.269 7406 Planarity : 0.005 0.054 8106 Dihedral : 7.354 93.857 6679 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.73 % Favored : 95.93 % Rotamer: Outliers : 5.36 % Allowed : 24.96 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.11), residues: 5922 helix: 1.99 (0.10), residues: 2352 sheet: -0.29 (0.13), residues: 1344 loop : -2.16 (0.11), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 70 TYR 0.040 0.002 TYR J 58 PHE 0.041 0.003 PHE F 232 HIS 0.009 0.003 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00738 (46816) covalent geometry : angle 0.79751 (63182) hydrogen bonds : bond 0.03910 ( 2733) hydrogen bonds : angle 4.91812 ( 7821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12864.52 seconds wall clock time: 220 minutes 9.14 seconds (13209.14 seconds total)