Starting phenix.real_space_refine on Fri Sep 19 02:10:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9b_38171/09_2025/8x9b_38171.cif" } resolution = 3.82 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= 0.015 sd= 0.218 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 140 5.16 5 C 14562 2.51 5 N 3762 2.21 5 O 4136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22600 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 185} Chain breaks: 2 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1698 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 192} Chain breaks: 2 Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1323 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain breaks: 3 Chain: "I" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1683 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 203} Chain breaks: 1 Chain: "K" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1625 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain breaks: 1 Chain: "M" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1590 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain breaks: 1 Chain: "O" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 870 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "P" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Restraints were copied for chains: F, H, J, L, N, Q, R, S Time building chain proxies: 5.10, per 1000 atoms: 0.23 Number of scatterers: 22600 At special positions: 0 Unit cell: (193.76, 148.96, 110.88, 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 140 16.00 O 4136 8.00 N 3762 7.00 C 14562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 93 " distance=2.06 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 93 " distance=2.06 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 50 sheets defined 9.6% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'D' and resid 116 through 125 removed outlier: 4.122A pdb=" N ARG D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.533A pdb=" N GLN D 172 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.889A pdb=" N PHE E 84 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.978A pdb=" N ARG E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 125 " --> pdb=" O ARG E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 173 removed outlier: 3.567A pdb=" N GLN E 172 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.694A pdb=" N VAL G 89 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 Processing helix chain 'G' and resid 171 through 178 removed outlier: 4.611A pdb=" N THR G 176 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.630A pdb=" N LEU I 86 " --> pdb=" O PRO I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 171 through 178 removed outlier: 4.358A pdb=" N THR I 176 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.700A pdb=" N ARG K 48 " --> pdb=" O GLU K 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL K 49 " --> pdb=" O ILE K 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 49' Processing helix chain 'K' and resid 64 through 70 removed outlier: 3.660A pdb=" N GLN K 67 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU K 69 " --> pdb=" O MET K 66 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS K 70 " --> pdb=" O GLN K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 98 Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'M' and resid 45 through 49 removed outlier: 3.713A pdb=" N ARG M 48 " --> pdb=" O GLU M 45 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL M 49 " --> pdb=" O ILE M 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 45 through 49' Processing helix chain 'M' and resid 64 through 70 removed outlier: 3.659A pdb=" N GLN M 67 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU M 69 " --> pdb=" O MET M 66 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS M 70 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 98 Processing helix chain 'M' and resid 99 through 105 Processing helix chain 'O' and resid 62 through 65 Processing helix chain 'P' and resid 84 through 88 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.953A pdb=" N PHE F 84 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER F 85 " --> pdb=" O ASN F 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 81 through 85' Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.122A pdb=" N ARG F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 125 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 removed outlier: 3.534A pdb=" N GLN F 172 " --> pdb=" O PHE F 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.888A pdb=" N PHE H 84 " --> pdb=" O GLY H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 125 removed outlier: 3.977A pdb=" N ARG H 120 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS H 122 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 125 " --> pdb=" O ARG H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 173 removed outlier: 3.567A pdb=" N GLN H 172 " --> pdb=" O PHE H 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 37 No H-bonds generated for 'chain 'J' and resid 35 through 37' Processing helix chain 'J' and resid 82 through 89 removed outlier: 3.694A pdb=" N VAL J 89 " --> pdb=" O VAL J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 166 Processing helix chain 'J' and resid 171 through 178 removed outlier: 4.611A pdb=" N THR J 176 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 37 No H-bonds generated for 'chain 'L' and resid 35 through 37' Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.629A pdb=" N LEU L 86 " --> pdb=" O PRO L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 166 Processing helix chain 'L' and resid 171 through 178 removed outlier: 4.358A pdb=" N THR L 176 " --> pdb=" O SER L 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 49 removed outlier: 3.700A pdb=" N ARG N 48 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL N 49 " --> pdb=" O ILE N 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 49' Processing helix chain 'N' and resid 64 through 70 removed outlier: 3.659A pdb=" N GLN N 67 " --> pdb=" O THR N 64 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU N 69 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS N 70 " --> pdb=" O GLN N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 98 Processing helix chain 'N' and resid 99 through 105 Processing helix chain 'Q' and resid 45 through 49 removed outlier: 3.713A pdb=" N ARG Q 48 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL Q 49 " --> pdb=" O ILE Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 45 through 49' Processing helix chain 'Q' and resid 64 through 70 removed outlier: 3.659A pdb=" N GLN Q 67 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU Q 69 " --> pdb=" O MET Q 66 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS Q 70 " --> pdb=" O GLN Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 98 Processing helix chain 'Q' and resid 99 through 105 Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'S' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'D' and resid 88 through 95 removed outlier: 6.004A pdb=" N LEU D 89 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET D 253 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER D 91 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 134 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL D 258 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG D 130 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA D 260 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR D 128 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 137 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA D 188 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 88 through 95 removed outlier: 6.004A pdb=" N LEU D 89 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET D 253 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER D 91 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 134 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL D 258 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG D 130 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA D 260 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR D 128 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 106 through 110 removed outlier: 3.669A pdb=" N THR D 232 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 179 " --> pdb=" O TYR D 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 88 through 95 removed outlier: 6.010A pdb=" N LEU E 89 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET E 253 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 91 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 134 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP E 132 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL E 258 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG E 130 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA E 260 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 128 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 137 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 188 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 88 through 95 removed outlier: 6.010A pdb=" N LEU E 89 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET E 253 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 91 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 134 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP E 132 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL E 258 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG E 130 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA E 260 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 128 " --> pdb=" O ALA E 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 106 through 107 removed outlier: 3.685A pdb=" N VAL E 181 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 179 " --> pdb=" O TYR E 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 32 through 33 removed outlier: 6.626A pdb=" N VAL G 32 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 32 through 33 removed outlier: 6.626A pdb=" N VAL G 32 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.685A pdb=" N ALA G 158 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 219 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA G 121 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN G 119 " --> pdb=" O PRO G 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.824A pdb=" N ILE I 18 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER I 21 " --> pdb=" O ILE I 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 32 through 33 removed outlier: 6.589A pdb=" N VAL I 32 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 193 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 64 through 65 removed outlier: 3.700A pdb=" N ARG I 103 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY I 105 " --> pdb=" O CYS I 242 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS I 242 " --> pdb=" O GLY I 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 158 through 159 removed outlier: 3.545A pdb=" N ALA I 158 " --> pdb=" O TYR I 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE I 212 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL I 219 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA I 121 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN I 119 " --> pdb=" O PRO I 221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 51 through 52 removed outlier: 6.796A pdb=" N GLY K 113 " --> pdb=" O TRP K 171 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP K 171 " --> pdb=" O GLY K 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 165 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 71 through 73 removed outlier: 6.526A pdb=" N TYR K 108 " --> pdb=" O CYS K 229 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS K 229 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN K 110 " --> pdb=" O LYS K 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 82 through 88 removed outlier: 6.742A pdb=" N ILE K 196 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA K 85 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE K 194 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG K 87 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY K 192 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR K 153 " --> pdb=" O TYR K 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 51 through 52 removed outlier: 6.789A pdb=" N GLY M 113 " --> pdb=" O TRP M 171 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP M 171 " --> pdb=" O GLY M 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL M 165 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 71 through 73 Processing sheet with id=AC1, first strand: chain 'M' and resid 82 through 88 removed outlier: 6.824A pdb=" N LEU M 82 " --> pdb=" O TYR M 198 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR M 198 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA M 84 " --> pdb=" O ILE M 196 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY M 192 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR M 153 " --> pdb=" O TYR M 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.650A pdb=" N GLU O 10 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR O 95 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 19 through 20 removed outlier: 3.762A pdb=" N ASP O 73 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 49 through 51 removed outlier: 3.671A pdb=" N TRP O 50 " --> pdb=" O MET O 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET O 59 " --> pdb=" O TRP O 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.590A pdb=" N ILE P 21 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.836A pdb=" N LEU P 11 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU P 110 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR P 91 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN P 43 " --> pdb=" O VAL P 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP P 40 " --> pdb=" O LEU P 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.836A pdb=" N LEU P 11 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU P 110 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR P 91 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR P 102 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 88 through 95 removed outlier: 6.003A pdb=" N LEU F 89 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET F 253 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER F 91 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 134 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 258 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG F 130 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA F 260 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR F 128 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 137 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 188 " --> pdb=" O PHE F 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 88 through 95 removed outlier: 6.003A pdb=" N LEU F 89 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET F 253 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER F 91 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 134 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 258 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG F 130 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA F 260 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR F 128 " --> pdb=" O ALA F 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 106 through 110 removed outlier: 3.670A pdb=" N THR F 232 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 179 " --> pdb=" O TYR F 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 88 through 95 removed outlier: 6.010A pdb=" N LEU H 89 " --> pdb=" O MET H 253 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET H 253 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER H 91 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 134 " --> pdb=" O ARG H 254 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP H 132 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 258 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG H 130 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA H 260 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR H 128 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 137 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 188 " --> pdb=" O PHE H 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 88 through 95 removed outlier: 6.010A pdb=" N LEU H 89 " --> pdb=" O MET H 253 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET H 253 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER H 91 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 134 " --> pdb=" O ARG H 254 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP H 132 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 258 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG H 130 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA H 260 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR H 128 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 106 through 107 removed outlier: 3.685A pdb=" N VAL H 181 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 179 " --> pdb=" O TYR H 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 32 through 33 removed outlier: 6.626A pdb=" N VAL J 32 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 32 through 33 removed outlier: 6.626A pdb=" N VAL J 32 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 158 through 159 removed outlier: 3.685A pdb=" N ALA J 158 " --> pdb=" O TYR J 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL J 219 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA J 121 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN J 119 " --> pdb=" O PRO J 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 14 through 18 removed outlier: 3.824A pdb=" N ILE L 18 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER L 21 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 32 through 33 removed outlier: 6.589A pdb=" N VAL L 32 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 193 " --> pdb=" O VAL L 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.700A pdb=" N ARG L 103 " --> pdb=" O GLU L 244 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY L 105 " --> pdb=" O CYS L 242 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS L 242 " --> pdb=" O GLY L 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.545A pdb=" N ALA L 158 " --> pdb=" O TYR L 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE L 212 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 219 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA L 121 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN L 119 " --> pdb=" O PRO L 221 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 51 through 52 removed outlier: 6.796A pdb=" N GLY N 113 " --> pdb=" O TRP N 171 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP N 171 " --> pdb=" O GLY N 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL N 165 " --> pdb=" O PHE N 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 71 through 73 removed outlier: 6.526A pdb=" N TYR N 108 " --> pdb=" O CYS N 229 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS N 229 " --> pdb=" O TYR N 108 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN N 110 " --> pdb=" O LYS N 227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 82 through 88 removed outlier: 6.742A pdb=" N ILE N 196 " --> pdb=" O CYS N 83 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA N 85 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE N 194 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG N 87 " --> pdb=" O GLY N 192 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY N 192 " --> pdb=" O ARG N 87 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR N 153 " --> pdb=" O TYR N 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 51 through 52 removed outlier: 6.789A pdb=" N GLY Q 113 " --> pdb=" O TRP Q 171 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP Q 171 " --> pdb=" O GLY Q 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL Q 165 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 71 through 73 Processing sheet with id=AE8, first strand: chain 'Q' and resid 82 through 88 removed outlier: 6.824A pdb=" N LEU Q 82 " --> pdb=" O TYR Q 198 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR Q 198 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA Q 84 " --> pdb=" O ILE Q 196 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY Q 192 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR Q 153 " --> pdb=" O TYR Q 135 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.650A pdb=" N GLU R 10 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR R 95 " --> pdb=" O VAL R 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 19 through 20 removed outlier: 3.762A pdb=" N ASP R 73 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 49 through 51 removed outlier: 3.671A pdb=" N TRP R 50 " --> pdb=" O MET R 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET R 59 " --> pdb=" O TRP R 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.591A pdb=" N ILE S 21 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.836A pdb=" N LEU S 11 " --> pdb=" O LYS S 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU S 110 " --> pdb=" O LEU S 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR S 91 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN S 43 " --> pdb=" O VAL S 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP S 40 " --> pdb=" O LEU S 52 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.836A pdb=" N LEU S 11 " --> pdb=" O LYS S 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU S 110 " --> pdb=" O LEU S 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR S 91 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR S 102 " --> pdb=" O GLN S 95 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1536 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: 4.93 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3630 1.31 - 1.44: 6544 1.44 - 1.56: 12846 1.56 - 1.69: 2 1.69 - 1.81: 212 Bond restraints: 23234 Sorted by residual: bond pdb=" N PRO G 163 " pdb=" CD PRO G 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.88e+01 bond pdb=" N PRO J 163 " pdb=" CD PRO J 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.79e+01 bond pdb=" CA LEU L 172 " pdb=" C LEU L 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA LEU I 172 " pdb=" C LEU I 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.19e-02 7.06e+03 3.67e+01 ... (remaining 23229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 30296 3.31 - 6.62: 1257 6.62 - 9.93: 141 9.93 - 13.24: 34 13.24 - 16.55: 18 Bond angle restraints: 31746 Sorted by residual: angle pdb=" N ALA O 101 " pdb=" CA ALA O 101 " pdb=" C ALA O 101 " ideal model delta sigma weight residual 111.36 127.05 -15.69 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N ALA R 101 " pdb=" CA ALA R 101 " pdb=" C ALA R 101 " ideal model delta sigma weight residual 111.36 127.03 -15.67 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N HIS L 145 " pdb=" CA HIS L 145 " pdb=" C HIS L 145 " ideal model delta sigma weight residual 108.13 95.41 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" N HIS I 145 " pdb=" CA HIS I 145 " pdb=" C HIS I 145 " ideal model delta sigma weight residual 108.13 95.42 12.71 9.00e-01 1.23e+00 1.99e+02 angle pdb=" N PHE G 82 " pdb=" CA PHE G 82 " pdb=" C PHE G 82 " ideal model delta sigma weight residual 112.35 128.90 -16.55 1.34e+00 5.57e-01 1.52e+02 ... (remaining 31741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 12666 17.30 - 34.60: 812 34.60 - 51.90: 120 51.90 - 69.20: 38 69.20 - 86.50: 20 Dihedral angle restraints: 13656 sinusoidal: 5286 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS S 23 " pdb=" SG CYS S 23 " pdb=" SG CYS S 93 " pdb=" CB CYS S 93 " ideal model delta sinusoidal sigma weight residual 93.00 150.82 -57.82 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 93 " pdb=" CB CYS P 93 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CA PHE G 82 " pdb=" CB PHE G 82 " ideal model delta harmonic sigma weight residual 122.80 133.63 -10.83 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 13653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3054 0.136 - 0.272: 477 0.272 - 0.409: 41 0.409 - 0.545: 6 0.545 - 0.681: 2 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CA PHE G 82 " pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CB PHE G 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE J 82 " pdb=" N PHE J 82 " pdb=" C PHE J 82 " pdb=" CB PHE J 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TRP F 261 " pdb=" N TRP F 261 " pdb=" C TRP F 261 " pdb=" CB TRP F 261 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 3577 not shown) Planarity restraints: 4038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR P 36 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR P 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR P 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR P 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR S 36 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR S 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR S 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR S 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 186 " 0.331 9.50e-02 1.11e+02 1.48e-01 1.36e+01 pdb=" NE ARG I 186 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG I 186 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG I 186 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 186 " 0.010 2.00e-02 2.50e+03 ... (remaining 4035 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1908 2.72 - 3.26: 20342 3.26 - 3.81: 33898 3.81 - 4.35: 39941 4.35 - 4.90: 71342 Nonbonded interactions: 167431 Sorted by model distance: nonbonded pdb=" N ALA I 168 " pdb=" O ALA I 168 " model vdw 2.173 2.496 nonbonded pdb=" N ALA L 168 " pdb=" O ALA L 168 " model vdw 2.174 2.496 nonbonded pdb=" N TRP O 104 " pdb=" O TRP O 104 " model vdw 2.267 2.496 nonbonded pdb=" N TRP R 104 " pdb=" O TRP R 104 " model vdw 2.267 2.496 nonbonded pdb=" N TYR D 116 " pdb=" O TYR D 116 " model vdw 2.289 2.496 ... (remaining 167426 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: 0.08 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.420 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.012 0.139 23238 Z= 0.836 Angle : 1.573 16.548 31754 Z= 1.020 Chirality : 0.100 0.681 3580 Planarity : 0.011 0.148 4038 Dihedral : 12.253 86.504 8260 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.14), residues: 2826 helix: -3.17 (0.40), residues: 124 sheet: -1.62 (0.17), residues: 844 loop : -2.19 (0.12), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG F 130 TYR 0.022 0.003 TYR N 107 PHE 0.024 0.003 PHE D 84 TRP 0.019 0.003 TRP S 40 HIS 0.006 0.001 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.01196 (23234) covalent geometry : angle 1.57240 (31746) SS BOND : bond 0.02169 ( 4) SS BOND : angle 3.62614 ( 8) hydrogen bonds : bond 0.29513 ( 534) hydrogen bonds : angle 8.80918 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1009 time to evaluate : 1.053 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: D 106 TYR cc_start: 0.7911 (p90) cc_final: 0.7595 (p90) REVERT: D 130 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7911 (ttt90) REVERT: D 143 ASN cc_start: 0.8713 (p0) cc_final: 0.8423 (p0) REVERT: D 183 MET cc_start: 0.8274 (ttm) cc_final: 0.7916 (mtp) REVERT: D 254 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8005 (mtp-110) REVERT: D 279 TYR cc_start: 0.8693 (p90) cc_final: 0.8217 (p90) REVERT: E 147 VAL cc_start: 0.8320 (t) cc_final: 0.7867 (m) REVERT: E 162 LYS cc_start: 0.8821 (mttt) cc_final: 0.8547 (mtpp) REVERT: E 276 ASN cc_start: 0.8050 (p0) cc_final: 0.7567 (p0) REVERT: G 31 ILE cc_start: 0.9281 (pt) cc_final: 0.8900 (mt) REVERT: G 127 LEU cc_start: 0.8502 (tp) cc_final: 0.8074 (tp) REVERT: I 30 ASN cc_start: 0.7501 (m-40) cc_final: 0.7099 (p0) REVERT: I 73 LYS cc_start: 0.9039 (tttp) cc_final: 0.8831 (tttp) REVERT: I 76 LYS cc_start: 0.8946 (mttt) cc_final: 0.8597 (mtpp) REVERT: I 84 ASP cc_start: 0.8314 (t70) cc_final: 0.7890 (t0) REVERT: I 198 MET cc_start: 0.8727 (ptp) cc_final: 0.8344 (ptp) REVERT: M 74 SER cc_start: 0.8495 (t) cc_final: 0.8208 (p) REVERT: M 120 MET cc_start: 0.8779 (ttm) cc_final: 0.8481 (ttm) REVERT: O 19 LYS cc_start: 0.7547 (ptmt) cc_final: 0.7074 (ptmm) REVERT: O 63 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7861 (mtmm) REVERT: O 71 THR cc_start: 0.7974 (t) cc_final: 0.7667 (p) REVERT: P 3 VAL cc_start: 0.8899 (t) cc_final: 0.8571 (m) REVERT: P 54 TYR cc_start: 0.6835 (t80) cc_final: 0.6369 (t80) REVERT: P 97 THR cc_start: 0.7721 (m) cc_final: 0.7512 (m) REVERT: F 254 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.8182 (mtp-110) REVERT: F 279 TYR cc_start: 0.8823 (p90) cc_final: 0.8598 (p90) REVERT: H 147 VAL cc_start: 0.8297 (t) cc_final: 0.8090 (p) REVERT: H 153 TYR cc_start: 0.9351 (m-80) cc_final: 0.9139 (m-80) REVERT: H 162 LYS cc_start: 0.8926 (mttt) cc_final: 0.8634 (mtpp) REVERT: H 276 ASN cc_start: 0.7986 (p0) cc_final: 0.7327 (p0) REVERT: J 31 ILE cc_start: 0.9304 (pt) cc_final: 0.8960 (mt) REVERT: J 216 VAL cc_start: 0.8594 (t) cc_final: 0.8362 (m) REVERT: L 30 ASN cc_start: 0.7501 (m-40) cc_final: 0.7146 (p0) REVERT: L 76 LYS cc_start: 0.8839 (mttt) cc_final: 0.8538 (mtpp) REVERT: L 84 ASP cc_start: 0.8333 (t70) cc_final: 0.7877 (t0) REVERT: L 198 MET cc_start: 0.8706 (ptp) cc_final: 0.8337 (ptp) REVERT: N 67 GLN cc_start: 0.9237 (mt0) cc_final: 0.9016 (mt0) REVERT: N 78 LYS cc_start: 0.8725 (mptt) cc_final: 0.8510 (mmmt) REVERT: N 172 ILE cc_start: 0.8880 (pt) cc_final: 0.8622 (pt) REVERT: N 173 SER cc_start: 0.9190 (p) cc_final: 0.8812 (m) REVERT: N 228 LEU cc_start: 0.8696 (tp) cc_final: 0.8437 (tp) REVERT: Q 120 MET cc_start: 0.8786 (ttm) cc_final: 0.8515 (ttm) REVERT: Q 224 PHE cc_start: 0.9170 (t80) cc_final: 0.8850 (t80) REVERT: R 19 LYS cc_start: 0.7513 (ptmt) cc_final: 0.7062 (ptmm) REVERT: R 63 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7805 (mtmm) REVERT: R 71 THR cc_start: 0.7981 (t) cc_final: 0.7713 (p) REVERT: S 3 VAL cc_start: 0.8838 (t) cc_final: 0.8479 (m) REVERT: S 31 TYR cc_start: 0.7687 (t80) cc_final: 0.7237 (t80) REVERT: S 38 VAL cc_start: 0.7199 (t) cc_final: 0.6974 (m) REVERT: S 54 TYR cc_start: 0.6812 (t80) cc_final: 0.6267 (t80) outliers start: 0 outliers final: 0 residues processed: 1009 average time/residue: 0.1796 time to fit residues: 273.9605 Evaluate side-chains 701 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 701 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 189 GLN D 269 GLN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 269 GLN G 118 HIS G 152 GLN G 225 ASN I 145 HIS I 174 GLN I 209 HIS K 12 GLN K 61 ASN K 97 GLN M 174 ASN P 6 GLN P 43 GLN F 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 189 GLN F 269 GLN F 278 ASN H 227 ASN H 228 ASN H 269 GLN J 118 HIS J 152 GLN J 225 ASN L 145 HIS L 155 GLN L 174 GLN L 209 HIS N 12 GLN N 61 ASN N 97 GLN Q 174 ASN S 6 GLN S 43 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115648 restraints weight = 37088.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119487 restraints weight = 20748.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121989 restraints weight = 14285.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123589 restraints weight = 11198.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124704 restraints weight = 9549.393| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 23238 Z= 0.139 Angle : 0.649 10.174 31754 Z= 0.336 Chirality : 0.047 0.198 3580 Planarity : 0.006 0.062 4038 Dihedral : 5.029 26.347 3096 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.09 % Allowed : 14.11 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.14), residues: 2826 helix: -3.48 (0.31), residues: 122 sheet: -1.19 (0.17), residues: 840 loop : -1.61 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 68 TYR 0.027 0.002 TYR P 92 PHE 0.025 0.001 PHE R 27 TRP 0.025 0.001 TRP E 171 HIS 0.005 0.001 HIS I 145 Details of bonding type rmsd covalent geometry : bond 0.00319 (23234) covalent geometry : angle 0.64929 (31746) SS BOND : bond 0.01067 ( 4) SS BOND : angle 1.14757 ( 8) hydrogen bonds : bond 0.04810 ( 534) hydrogen bonds : angle 6.08630 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 737 time to evaluate : 0.920 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: D 76 GLN cc_start: 0.8837 (tp40) cc_final: 0.8511 (tp-100) REVERT: D 143 ASN cc_start: 0.8814 (p0) cc_final: 0.8408 (p0) REVERT: D 205 TYR cc_start: 0.8042 (t80) cc_final: 0.7750 (t80) REVERT: D 278 ASN cc_start: 0.8328 (m110) cc_final: 0.8095 (m110) REVERT: D 279 TYR cc_start: 0.8653 (p90) cc_final: 0.8241 (p90) REVERT: E 119 LEU cc_start: 0.8735 (tp) cc_final: 0.8504 (tp) REVERT: E 147 VAL cc_start: 0.8465 (t) cc_final: 0.7969 (p) REVERT: E 149 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7745 (tp40) REVERT: E 162 LYS cc_start: 0.8857 (mttt) cc_final: 0.8593 (mtpp) REVERT: E 183 MET cc_start: 0.8887 (ttm) cc_final: 0.8370 (ttm) REVERT: G 62 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7214 (mmm160) REVERT: G 74 ASP cc_start: 0.7242 (p0) cc_final: 0.7008 (p0) REVERT: G 104 SER cc_start: 0.8898 (t) cc_final: 0.8669 (m) REVERT: G 127 LEU cc_start: 0.8366 (tp) cc_final: 0.8097 (tp) REVERT: G 130 TYR cc_start: 0.8780 (t80) cc_final: 0.8533 (t80) REVERT: G 199 ASN cc_start: 0.8971 (t0) cc_final: 0.8675 (t0) REVERT: G 231 GLU cc_start: 0.8455 (pt0) cc_final: 0.8223 (pt0) REVERT: I 223 ASP cc_start: 0.8555 (t0) cc_final: 0.8193 (m-30) REVERT: K 28 PHE cc_start: 0.8177 (t80) cc_final: 0.7826 (t80) REVERT: K 78 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8521 (mmmt) REVERT: K 226 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7546 (mtt) REVERT: O 3 GLN cc_start: 0.7584 (pt0) cc_final: 0.7365 (pm20) REVERT: O 19 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7852 (ptmm) REVERT: P 97 THR cc_start: 0.8702 (m) cc_final: 0.8464 (p) REVERT: F 76 GLN cc_start: 0.8759 (tp40) cc_final: 0.8400 (tp-100) REVERT: F 143 ASN cc_start: 0.8744 (p0) cc_final: 0.8404 (p0) REVERT: F 278 ASN cc_start: 0.8479 (m-40) cc_final: 0.8186 (m110) REVERT: F 279 TYR cc_start: 0.8785 (p90) cc_final: 0.8559 (p90) REVERT: H 119 LEU cc_start: 0.8734 (tp) cc_final: 0.8532 (tp) REVERT: H 147 VAL cc_start: 0.8442 (t) cc_final: 0.8053 (p) REVERT: H 149 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7765 (tm-30) REVERT: H 154 MET cc_start: 0.8269 (ttp) cc_final: 0.8045 (ttm) REVERT: H 162 LYS cc_start: 0.8852 (mttt) cc_final: 0.8618 (mtpp) REVERT: H 183 MET cc_start: 0.8816 (ttm) cc_final: 0.8294 (ttm) REVERT: H 275 THR cc_start: 0.8931 (p) cc_final: 0.8658 (t) REVERT: J 62 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7128 (mmm160) REVERT: J 127 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8213 (tp) REVERT: J 164 TYR cc_start: 0.9206 (t80) cc_final: 0.8952 (t80) REVERT: J 199 ASN cc_start: 0.9004 (t0) cc_final: 0.8686 (t0) REVERT: J 231 GLU cc_start: 0.8392 (pt0) cc_final: 0.8134 (pt0) REVERT: L 76 LYS cc_start: 0.8742 (mttt) cc_final: 0.8518 (mtpp) REVERT: Q 48 ARG cc_start: 0.8493 (mtt90) cc_final: 0.7825 (mtt-85) REVERT: Q 78 LYS cc_start: 0.7874 (tmtt) cc_final: 0.7626 (tmtt) REVERT: R 19 LYS cc_start: 0.8125 (ptmt) cc_final: 0.7819 (ptmm) REVERT: R 63 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8826 (mtmm) REVERT: S 38 VAL cc_start: 0.8530 (t) cc_final: 0.8325 (m) outliers start: 77 outliers final: 48 residues processed: 770 average time/residue: 0.1706 time to fit residues: 202.7849 Evaluate side-chains 690 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 640 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 286 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 226 MET Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 186 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN E 118 GLN E 227 ASN E 276 ASN G 152 GLN I 145 HIS I 208 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 ASN P 6 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN H 118 GLN H 227 ASN H 276 ASN J 152 GLN J 211 ASN L 145 HIS ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 ASN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN Q 103 GLN ** Q 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN R 57 ASN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113494 restraints weight = 37400.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117360 restraints weight = 21093.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119915 restraints weight = 14651.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121592 restraints weight = 11526.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122685 restraints weight = 9829.623| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23238 Z= 0.122 Angle : 0.591 9.141 31754 Z= 0.300 Chirality : 0.045 0.201 3580 Planarity : 0.005 0.055 4038 Dihedral : 4.700 25.306 3096 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.26 % Allowed : 16.04 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 2826 helix: -3.22 (0.35), residues: 122 sheet: -0.86 (0.17), residues: 836 loop : -1.30 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 68 TYR 0.024 0.001 TYR J 79 PHE 0.026 0.001 PHE O 27 TRP 0.038 0.001 TRP E 171 HIS 0.004 0.001 HIS L 145 Details of bonding type rmsd covalent geometry : bond 0.00280 (23234) covalent geometry : angle 0.59061 (31746) SS BOND : bond 0.00792 ( 4) SS BOND : angle 1.73511 ( 8) hydrogen bonds : bond 0.03957 ( 534) hydrogen bonds : angle 5.46922 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 672 time to evaluate : 0.812 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: D 76 GLN cc_start: 0.8820 (tp40) cc_final: 0.8616 (tp-100) REVERT: D 143 ASN cc_start: 0.8816 (p0) cc_final: 0.8326 (p0) REVERT: D 185 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7736 (t0) REVERT: D 278 ASN cc_start: 0.8534 (m110) cc_final: 0.8321 (m110) REVERT: D 279 TYR cc_start: 0.8623 (p90) cc_final: 0.8263 (p90) REVERT: E 119 LEU cc_start: 0.8705 (tp) cc_final: 0.8452 (tp) REVERT: E 147 VAL cc_start: 0.8614 (t) cc_final: 0.8330 (p) REVERT: E 162 LYS cc_start: 0.8867 (mttt) cc_final: 0.8606 (mtpp) REVERT: E 183 MET cc_start: 0.8952 (ttm) cc_final: 0.8630 (ttm) REVERT: G 30 ASN cc_start: 0.7959 (m-40) cc_final: 0.7724 (t0) REVERT: G 62 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7255 (mmm160) REVERT: G 104 SER cc_start: 0.8988 (t) cc_final: 0.8542 (m) REVERT: G 127 LEU cc_start: 0.8435 (tp) cc_final: 0.8134 (tp) REVERT: G 130 TYR cc_start: 0.8816 (t80) cc_final: 0.8554 (t80) REVERT: G 199 ASN cc_start: 0.9074 (t0) cc_final: 0.8605 (t0) REVERT: G 231 GLU cc_start: 0.8420 (pt0) cc_final: 0.8175 (pt0) REVERT: K 62 GLU cc_start: 0.8410 (mp0) cc_final: 0.8121 (mp0) REVERT: K 78 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8675 (mmmt) REVERT: K 226 MET cc_start: 0.7886 (mtt) cc_final: 0.7618 (mtt) REVERT: M 48 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8344 (mmt90) REVERT: O 19 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7910 (ptmm) REVERT: O 63 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8902 (mtmm) REVERT: P 4 MET cc_start: 0.8730 (mmm) cc_final: 0.8410 (mmm) REVERT: P 54 TYR cc_start: 0.7062 (t80) cc_final: 0.6674 (t80) REVERT: P 112 LYS cc_start: 0.4950 (tptt) cc_final: 0.4343 (tppt) REVERT: F 76 GLN cc_start: 0.8717 (tp40) cc_final: 0.8503 (tp-100) REVERT: F 95 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: F 185 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (t0) REVERT: F 278 ASN cc_start: 0.8521 (m-40) cc_final: 0.8248 (m110) REVERT: H 147 VAL cc_start: 0.8573 (t) cc_final: 0.8166 (p) REVERT: H 149 GLN cc_start: 0.8278 (tp-100) cc_final: 0.7787 (tm-30) REVERT: H 162 LYS cc_start: 0.8902 (mttt) cc_final: 0.8641 (mtpp) REVERT: H 183 MET cc_start: 0.8924 (ttm) cc_final: 0.8315 (ttm) REVERT: H 275 THR cc_start: 0.8758 (p) cc_final: 0.8488 (t) REVERT: J 74 ASP cc_start: 0.7339 (p0) cc_final: 0.7082 (p0) REVERT: J 81 LYS cc_start: 0.8795 (mttm) cc_final: 0.8537 (mttm) REVERT: J 127 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8257 (tp) REVERT: J 199 ASN cc_start: 0.9126 (t0) cc_final: 0.8574 (t0) REVERT: J 231 GLU cc_start: 0.8365 (pt0) cc_final: 0.8124 (pt0) REVERT: L 76 LYS cc_start: 0.8736 (mttt) cc_final: 0.8512 (mtpp) REVERT: N 14 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9084 (tp) REVERT: Q 48 ARG cc_start: 0.8447 (mtt90) cc_final: 0.7914 (mtt-85) REVERT: R 19 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7875 (ptmm) REVERT: R 63 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8879 (mtmm) REVERT: S 54 TYR cc_start: 0.7064 (t80) cc_final: 0.6583 (t80) REVERT: S 79 LYS cc_start: 0.6508 (mmmt) cc_final: 0.5869 (mmtm) outliers start: 106 outliers final: 77 residues processed: 719 average time/residue: 0.1709 time to fit residues: 189.0938 Evaluate side-chains 718 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 636 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 208 ASN Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP Chi-restraints excluded: chain S residue 42 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 270 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN I 208 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN P 95 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 149 GLN H 227 ASN J 152 GLN N 12 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS N 162 GLN ** Q 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102695 restraints weight = 38328.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106163 restraints weight = 22310.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108460 restraints weight = 15810.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109948 restraints weight = 12598.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110952 restraints weight = 10857.919| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 23238 Z= 0.384 Angle : 0.801 11.921 31754 Z= 0.412 Chirality : 0.052 0.202 3580 Planarity : 0.006 0.057 4038 Dihedral : 5.600 27.504 3096 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.15 % Allowed : 16.60 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.14), residues: 2826 helix: -3.04 (0.35), residues: 122 sheet: -1.04 (0.17), residues: 838 loop : -1.56 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 68 TYR 0.028 0.003 TYR S 54 PHE 0.030 0.003 PHE Q 71 TRP 0.048 0.002 TRP E 171 HIS 0.040 0.002 HIS I 145 Details of bonding type rmsd covalent geometry : bond 0.00921 (23234) covalent geometry : angle 0.80002 (31746) SS BOND : bond 0.00774 ( 4) SS BOND : angle 2.62875 ( 8) hydrogen bonds : bond 0.05059 ( 534) hydrogen bonds : angle 5.80111 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 653 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8879 (tp40) cc_final: 0.8650 (tp40) REVERT: D 95 MET cc_start: 0.7947 (ttp) cc_final: 0.7675 (tmm) REVERT: D 153 TYR cc_start: 0.7774 (m-10) cc_final: 0.7531 (m-10) REVERT: E 110 ASP cc_start: 0.9078 (t0) cc_final: 0.8813 (t0) REVERT: E 162 LYS cc_start: 0.8940 (mttt) cc_final: 0.8645 (mtpp) REVERT: E 202 GLN cc_start: 0.8201 (mt0) cc_final: 0.7876 (mt0) REVERT: G 30 ASN cc_start: 0.8264 (m-40) cc_final: 0.7938 (t0) REVERT: G 199 ASN cc_start: 0.9049 (t0) cc_final: 0.8614 (t0) REVERT: G 231 GLU cc_start: 0.8533 (pt0) cc_final: 0.8294 (pt0) REVERT: I 144 SER cc_start: 0.8903 (m) cc_final: 0.8578 (t) REVERT: I 241 MET cc_start: 0.8036 (mmm) cc_final: 0.7607 (mtp) REVERT: K 50 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6227 (mm-30) REVERT: K 62 GLU cc_start: 0.8629 (mp0) cc_final: 0.8397 (mp0) REVERT: K 78 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8734 (mmmt) REVERT: K 231 ASP cc_start: 0.8780 (t70) cc_final: 0.8438 (t0) REVERT: M 50 GLU cc_start: 0.8069 (pm20) cc_final: 0.7573 (pm20) REVERT: O 19 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8159 (ptmm) REVERT: O 63 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8880 (mtmm) REVERT: P 54 TYR cc_start: 0.7247 (t80) cc_final: 0.7010 (t80) REVERT: P 80 ILE cc_start: 0.7639 (mt) cc_final: 0.7380 (mm) REVERT: F 76 GLN cc_start: 0.8834 (tp40) cc_final: 0.8493 (tm-30) REVERT: F 82 ASN cc_start: 0.8934 (m110) cc_final: 0.8686 (m-40) REVERT: F 95 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: F 195 MET cc_start: 0.7148 (mmm) cc_final: 0.6724 (mmm) REVERT: H 110 ASP cc_start: 0.9078 (t0) cc_final: 0.8803 (t0) REVERT: H 118 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8483 (tp-100) REVERT: H 162 LYS cc_start: 0.8944 (mttt) cc_final: 0.8661 (mtpp) REVERT: H 222 TYR cc_start: 0.6249 (m-10) cc_final: 0.6028 (m-10) REVERT: J 30 ASN cc_start: 0.8222 (m-40) cc_final: 0.7857 (t0) REVERT: J 82 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6845 (t80) REVERT: J 104 SER cc_start: 0.9185 (t) cc_final: 0.8976 (p) REVERT: J 127 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8395 (tp) REVERT: J 199 ASN cc_start: 0.9094 (t0) cc_final: 0.8596 (t0) REVERT: J 231 GLU cc_start: 0.8522 (pt0) cc_final: 0.8258 (pt0) REVERT: L 76 LYS cc_start: 0.8935 (mttt) cc_final: 0.8728 (mtpp) REVERT: L 241 MET cc_start: 0.8061 (mmm) cc_final: 0.7605 (mtp) REVERT: N 14 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9211 (tp) REVERT: Q 67 GLN cc_start: 0.9061 (mt0) cc_final: 0.8853 (mt0) REVERT: R 19 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8141 (ptmm) REVERT: R 59 MET cc_start: 0.6994 (ttt) cc_final: 0.6405 (ttt) REVERT: S 54 TYR cc_start: 0.7134 (t80) cc_final: 0.6867 (t80) REVERT: S 79 LYS cc_start: 0.6769 (mmmt) cc_final: 0.6180 (mmtm) outliers start: 153 outliers final: 113 residues processed: 743 average time/residue: 0.1694 time to fit residues: 195.5795 Evaluate side-chains 731 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 613 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 286 CYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 143 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 190 CYS Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 162 GLN Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 64 optimal weight: 0.0670 chunk 30 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 245 HIS D 276 ASN E 118 GLN E 149 GLN E 227 ASN G 109 HIS G 152 GLN I 155 GLN K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN J 152 GLN N 12 GLN N 97 GLN Q 199 GLN S 95 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109152 restraints weight = 37266.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112833 restraints weight = 21112.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115267 restraints weight = 14731.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116882 restraints weight = 11609.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117716 restraints weight = 9893.184| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23238 Z= 0.114 Angle : 0.591 8.206 31754 Z= 0.300 Chirality : 0.045 0.201 3580 Planarity : 0.005 0.050 4038 Dihedral : 4.931 25.392 3096 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.86 % Allowed : 20.66 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 2826 helix: -2.93 (0.37), residues: 124 sheet: -0.72 (0.17), residues: 806 loop : -1.20 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 236 TYR 0.025 0.001 TYR F 106 PHE 0.022 0.001 PHE E 273 TRP 0.021 0.001 TRP E 171 HIS 0.004 0.001 HIS G 162 Details of bonding type rmsd covalent geometry : bond 0.00257 (23234) covalent geometry : angle 0.59108 (31746) SS BOND : bond 0.00447 ( 4) SS BOND : angle 0.94570 ( 8) hydrogen bonds : bond 0.03652 ( 534) hydrogen bonds : angle 5.40524 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 621 time to evaluate : 0.921 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: D 76 GLN cc_start: 0.8769 (tp40) cc_final: 0.8500 (tp-100) REVERT: E 110 ASP cc_start: 0.9022 (t0) cc_final: 0.8789 (t0) REVERT: E 162 LYS cc_start: 0.8912 (mttt) cc_final: 0.8588 (mtpp) REVERT: E 183 MET cc_start: 0.8802 (ttm) cc_final: 0.8303 (ttm) REVERT: E 202 GLN cc_start: 0.8006 (mt0) cc_final: 0.7780 (mt0) REVERT: E 280 LYS cc_start: 0.8684 (tttt) cc_final: 0.8356 (tppt) REVERT: G 30 ASN cc_start: 0.8114 (m-40) cc_final: 0.7791 (t0) REVERT: G 199 ASN cc_start: 0.9080 (t0) cc_final: 0.8653 (t0) REVERT: G 231 GLU cc_start: 0.8448 (pt0) cc_final: 0.8215 (pt0) REVERT: I 84 ASP cc_start: 0.8029 (t0) cc_final: 0.7586 (t0) REVERT: I 100 TYR cc_start: 0.6574 (t80) cc_final: 0.6270 (t80) REVERT: I 152 GLN cc_start: 0.8436 (mm110) cc_final: 0.8009 (mm110) REVERT: I 241 MET cc_start: 0.7969 (mmm) cc_final: 0.7478 (mtp) REVERT: K 62 GLU cc_start: 0.8593 (mp0) cc_final: 0.8353 (mp0) REVERT: M 48 ARG cc_start: 0.8625 (mtt90) cc_final: 0.8214 (mmt90) REVERT: M 50 GLU cc_start: 0.8017 (pm20) cc_final: 0.7597 (pm20) REVERT: O 19 LYS cc_start: 0.8325 (ptmt) cc_final: 0.8081 (ptmt) REVERT: O 59 MET cc_start: 0.7188 (ttt) cc_final: 0.6814 (ttp) REVERT: O 63 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8880 (mtmm) REVERT: P 54 TYR cc_start: 0.7122 (t80) cc_final: 0.6896 (t80) REVERT: P 80 ILE cc_start: 0.7212 (mt) cc_final: 0.6887 (mm) REVERT: F 76 GLN cc_start: 0.8750 (tp40) cc_final: 0.8357 (tm-30) REVERT: F 82 ASN cc_start: 0.8919 (m110) cc_final: 0.8613 (m-40) REVERT: F 230 MET cc_start: 0.7090 (ptp) cc_final: 0.6862 (ptp) REVERT: F 253 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: H 110 ASP cc_start: 0.9031 (t0) cc_final: 0.8768 (t0) REVERT: H 118 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8309 (tp-100) REVERT: H 162 LYS cc_start: 0.8920 (mttt) cc_final: 0.8613 (mtpp) REVERT: H 183 MET cc_start: 0.8786 (ttm) cc_final: 0.8289 (ttm) REVERT: H 275 THR cc_start: 0.8803 (p) cc_final: 0.8496 (t) REVERT: H 280 LYS cc_start: 0.8583 (tttt) cc_final: 0.8248 (tppt) REVERT: J 30 ASN cc_start: 0.8242 (m-40) cc_final: 0.7892 (t0) REVERT: J 81 LYS cc_start: 0.8923 (mttm) cc_final: 0.8708 (mttm) REVERT: J 197 TYR cc_start: 0.8569 (t80) cc_final: 0.8303 (t80) REVERT: J 199 ASN cc_start: 0.9137 (t0) cc_final: 0.8498 (t0) REVERT: J 231 GLU cc_start: 0.8443 (pt0) cc_final: 0.8199 (pt0) REVERT: L 76 LYS cc_start: 0.8694 (mttt) cc_final: 0.8428 (mtpp) REVERT: L 241 MET cc_start: 0.7980 (mmm) cc_final: 0.7478 (mtp) REVERT: N 14 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9137 (tp) REVERT: N 78 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8425 (mmtm) REVERT: Q 48 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8445 (mtt90) REVERT: R 19 LYS cc_start: 0.8316 (ptmt) cc_final: 0.8009 (ptmt) REVERT: R 63 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8928 (mtmm) REVERT: S 79 LYS cc_start: 0.6536 (mmmt) cc_final: 0.5934 (mmtm) outliers start: 96 outliers final: 56 residues processed: 679 average time/residue: 0.1719 time to fit residues: 179.8247 Evaluate side-chains 651 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 593 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 39 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 24 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 101 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN E 118 GLN E 227 ASN G 152 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 227 ASN J 152 GLN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106042 restraints weight = 36978.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109702 restraints weight = 21560.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112091 restraints weight = 15329.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113636 restraints weight = 12282.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114650 restraints weight = 10621.441| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 23238 Z= 0.283 Angle : 0.683 9.868 31754 Z= 0.348 Chirality : 0.048 0.197 3580 Planarity : 0.005 0.052 4038 Dihedral : 5.192 27.198 3096 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.23 % Allowed : 19.41 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.15), residues: 2826 helix: -2.78 (0.37), residues: 138 sheet: -0.86 (0.17), residues: 826 loop : -1.31 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 69 TYR 0.027 0.002 TYR S 54 PHE 0.024 0.002 PHE K 28 TRP 0.021 0.002 TRP E 171 HIS 0.005 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00677 (23234) covalent geometry : angle 0.68225 (31746) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.37248 ( 8) hydrogen bonds : bond 0.04238 ( 534) hydrogen bonds : angle 5.52588 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 605 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8863 (tp40) cc_final: 0.8378 (tm-30) REVERT: D 95 MET cc_start: 0.7817 (ttp) cc_final: 0.7519 (tmm) REVERT: E 110 ASP cc_start: 0.9128 (t0) cc_final: 0.8824 (t0) REVERT: E 162 LYS cc_start: 0.9014 (mttt) cc_final: 0.8650 (mtpp) REVERT: E 183 MET cc_start: 0.8819 (ttm) cc_final: 0.8206 (ttm) REVERT: E 202 GLN cc_start: 0.8194 (mt0) cc_final: 0.7947 (mt0) REVERT: E 206 ASP cc_start: 0.8742 (t70) cc_final: 0.8431 (t0) REVERT: E 222 TYR cc_start: 0.6300 (m-10) cc_final: 0.5898 (m-10) REVERT: E 253 MET cc_start: 0.8327 (ttm) cc_final: 0.7864 (ttp) REVERT: G 199 ASN cc_start: 0.9058 (t0) cc_final: 0.8627 (t0) REVERT: G 231 GLU cc_start: 0.8559 (pt0) cc_final: 0.8160 (pt0) REVERT: I 102 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7204 (p90) REVERT: I 241 MET cc_start: 0.7928 (mmm) cc_final: 0.7457 (mtp) REVERT: K 62 GLU cc_start: 0.8781 (mp0) cc_final: 0.8455 (mp0) REVERT: M 48 ARG cc_start: 0.8676 (mtt90) cc_final: 0.8358 (mtt90) REVERT: M 50 GLU cc_start: 0.8153 (pm20) cc_final: 0.7719 (pm20) REVERT: O 19 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8183 (ptmt) REVERT: O 59 MET cc_start: 0.7134 (ttt) cc_final: 0.6489 (ttp) REVERT: O 63 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8884 (mtmm) REVERT: P 54 TYR cc_start: 0.7230 (t80) cc_final: 0.7028 (t80) REVERT: P 80 ILE cc_start: 0.7565 (mt) cc_final: 0.7254 (mm) REVERT: P 112 LYS cc_start: 0.5890 (tptt) cc_final: 0.5690 (tptt) REVERT: F 76 GLN cc_start: 0.8786 (tp40) cc_final: 0.8429 (tm-30) REVERT: F 82 ASN cc_start: 0.8956 (m110) cc_final: 0.8729 (m-40) REVERT: F 95 MET cc_start: 0.7619 (mmm) cc_final: 0.7324 (mmm) REVERT: H 106 TYR cc_start: 0.8637 (p90) cc_final: 0.8384 (p90) REVERT: H 107 VAL cc_start: 0.9134 (t) cc_final: 0.8788 (m) REVERT: H 110 ASP cc_start: 0.9126 (t0) cc_final: 0.8829 (t0) REVERT: H 162 LYS cc_start: 0.8987 (mttt) cc_final: 0.8644 (mtpp) REVERT: H 183 MET cc_start: 0.8801 (ttm) cc_final: 0.8302 (ttm) REVERT: H 222 TYR cc_start: 0.6264 (m-10) cc_final: 0.5989 (m-10) REVERT: J 30 ASN cc_start: 0.8177 (m-40) cc_final: 0.7772 (t0) REVERT: J 199 ASN cc_start: 0.9095 (t0) cc_final: 0.8542 (t0) REVERT: J 231 GLU cc_start: 0.8541 (pt0) cc_final: 0.8071 (pt0) REVERT: L 76 LYS cc_start: 0.8868 (mttt) cc_final: 0.8646 (mtpp) REVERT: L 102 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7163 (p90) REVERT: L 241 MET cc_start: 0.7927 (mmm) cc_final: 0.7472 (mtp) REVERT: N 14 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9206 (tp) REVERT: N 68 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8799 (mmm160) REVERT: Q 50 GLU cc_start: 0.8153 (pm20) cc_final: 0.7723 (pm20) REVERT: Q 78 LYS cc_start: 0.7779 (tmtt) cc_final: 0.7421 (tmtt) REVERT: R 19 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8164 (ptmt) REVERT: S 25 SER cc_start: 0.8354 (m) cc_final: 0.8070 (p) REVERT: S 79 LYS cc_start: 0.6679 (mmmt) cc_final: 0.6025 (mmtm) REVERT: S 112 LYS cc_start: 0.5837 (tptt) cc_final: 0.5594 (tptt) outliers start: 130 outliers final: 102 residues processed: 680 average time/residue: 0.1735 time to fit residues: 181.9411 Evaluate side-chains 701 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 596 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 190 CYS Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 144 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN E 118 GLN E 227 ASN E 276 ASN G 152 GLN I 155 GLN K 67 GLN K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 118 GLN H 202 GLN H 227 ASN J 152 GLN N 97 GLN N 199 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098099 restraints weight = 37611.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101868 restraints weight = 21330.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104336 restraints weight = 14965.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105951 restraints weight = 11899.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107006 restraints weight = 10234.199| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23238 Z= 0.134 Angle : 0.594 9.658 31754 Z= 0.301 Chirality : 0.045 0.187 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.870 25.208 3096 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.34 % Allowed : 21.14 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.15), residues: 2826 helix: -2.29 (0.48), residues: 104 sheet: -0.75 (0.17), residues: 820 loop : -1.13 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 236 TYR 0.025 0.001 TYR F 106 PHE 0.026 0.001 PHE K 28 TRP 0.020 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00321 (23234) covalent geometry : angle 0.59391 (31746) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.07026 ( 8) hydrogen bonds : bond 0.03549 ( 534) hydrogen bonds : angle 5.33758 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 602 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8789 (tp40) cc_final: 0.8373 (tm-30) REVERT: D 95 MET cc_start: 0.7677 (ttp) cc_final: 0.7349 (tmm) REVERT: D 182 LYS cc_start: 0.7213 (mtmt) cc_final: 0.7001 (ttmt) REVERT: D 202 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: E 110 ASP cc_start: 0.9113 (t0) cc_final: 0.8800 (t0) REVERT: E 162 LYS cc_start: 0.9018 (mttt) cc_final: 0.8614 (mtpp) REVERT: E 183 MET cc_start: 0.8812 (ttm) cc_final: 0.8129 (ttm) REVERT: E 206 ASP cc_start: 0.8708 (t70) cc_final: 0.8358 (t0) REVERT: E 222 TYR cc_start: 0.6326 (m-10) cc_final: 0.5815 (m-10) REVERT: E 236 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7347 (ptt180) REVERT: E 253 MET cc_start: 0.8357 (ttm) cc_final: 0.7901 (ttp) REVERT: E 278 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8477 (m-40) REVERT: G 199 ASN cc_start: 0.9014 (t0) cc_final: 0.8598 (t0) REVERT: G 231 GLU cc_start: 0.8553 (pt0) cc_final: 0.8169 (pt0) REVERT: I 84 ASP cc_start: 0.8119 (t0) cc_final: 0.7680 (t0) REVERT: I 102 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7010 (p90) REVERT: I 152 GLN cc_start: 0.8472 (mm110) cc_final: 0.8007 (mm110) REVERT: I 241 MET cc_start: 0.7764 (mmm) cc_final: 0.7324 (mtp) REVERT: K 62 GLU cc_start: 0.8863 (mp0) cc_final: 0.8468 (mp0) REVERT: M 48 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8350 (mtt90) REVERT: M 50 GLU cc_start: 0.8256 (pm20) cc_final: 0.7811 (pm20) REVERT: O 19 LYS cc_start: 0.8364 (ptmt) cc_final: 0.8011 (ptmm) REVERT: O 59 MET cc_start: 0.7205 (ttt) cc_final: 0.6425 (ttp) REVERT: O 63 LYS cc_start: 0.9261 (mtmt) cc_final: 0.8905 (mtmm) REVERT: O 73 ASP cc_start: 0.8129 (t0) cc_final: 0.7375 (t0) REVERT: P 54 TYR cc_start: 0.7225 (t80) cc_final: 0.6986 (t80) REVERT: P 80 ILE cc_start: 0.7142 (mt) cc_final: 0.6723 (mm) REVERT: F 76 GLN cc_start: 0.8756 (tp40) cc_final: 0.8427 (tm-30) REVERT: F 82 ASN cc_start: 0.8892 (m110) cc_final: 0.8673 (m-40) REVERT: F 253 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: H 107 VAL cc_start: 0.9060 (t) cc_final: 0.8681 (m) REVERT: H 110 ASP cc_start: 0.9100 (t0) cc_final: 0.8807 (t0) REVERT: H 162 LYS cc_start: 0.8963 (mttt) cc_final: 0.8585 (mtpp) REVERT: H 183 MET cc_start: 0.8839 (ttm) cc_final: 0.8271 (ttm) REVERT: H 280 LYS cc_start: 0.8726 (tttt) cc_final: 0.8269 (tppt) REVERT: J 30 ASN cc_start: 0.8171 (m-40) cc_final: 0.7733 (t0) REVERT: J 199 ASN cc_start: 0.9066 (t0) cc_final: 0.8526 (t0) REVERT: J 231 GLU cc_start: 0.8542 (pt0) cc_final: 0.8181 (pt0) REVERT: L 76 LYS cc_start: 0.8758 (mttt) cc_final: 0.8460 (mtpp) REVERT: L 102 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7017 (p90) REVERT: L 241 MET cc_start: 0.7763 (mmm) cc_final: 0.7343 (mtp) REVERT: N 68 ARG cc_start: 0.9183 (mtp85) cc_final: 0.8811 (mmm160) REVERT: Q 48 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8458 (mtt90) REVERT: Q 78 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7316 (tmtt) REVERT: R 19 LYS cc_start: 0.8330 (ptmt) cc_final: 0.7987 (ptmm) REVERT: R 63 LYS cc_start: 0.9281 (mtmm) cc_final: 0.8939 (mtmm) REVERT: S 25 SER cc_start: 0.8503 (m) cc_final: 0.8061 (p) REVERT: S 79 LYS cc_start: 0.6544 (mmmt) cc_final: 0.5879 (mmtm) outliers start: 108 outliers final: 76 residues processed: 675 average time/residue: 0.1721 time to fit residues: 179.0753 Evaluate side-chains 668 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 587 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 163 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 258 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN E 227 ASN E 276 ASN G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 118 GLN H 227 ASN J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109359 restraints weight = 36612.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113018 restraints weight = 21001.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115452 restraints weight = 14879.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117038 restraints weight = 11884.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118074 restraints weight = 10236.754| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23238 Z= 0.151 Angle : 0.597 10.156 31754 Z= 0.302 Chirality : 0.045 0.168 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.791 25.208 3096 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.98 % Allowed : 21.50 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.15), residues: 2826 helix: -2.14 (0.49), residues: 104 sheet: -0.70 (0.18), residues: 804 loop : -1.08 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 87 TYR 0.027 0.002 TYR D 106 PHE 0.028 0.001 PHE K 28 TRP 0.014 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00364 (23234) covalent geometry : angle 0.59720 (31746) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.16423 ( 8) hydrogen bonds : bond 0.03532 ( 534) hydrogen bonds : angle 5.28147 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 592 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8722 (tp40) cc_final: 0.8442 (tm-30) REVERT: D 95 MET cc_start: 0.7653 (ttp) cc_final: 0.7325 (tmm) REVERT: E 110 ASP cc_start: 0.9105 (t0) cc_final: 0.8789 (t0) REVERT: E 162 LYS cc_start: 0.9021 (mttt) cc_final: 0.8614 (mtpp) REVERT: E 183 MET cc_start: 0.8763 (ttm) cc_final: 0.8129 (ttm) REVERT: E 206 ASP cc_start: 0.8713 (t70) cc_final: 0.8375 (t0) REVERT: E 222 TYR cc_start: 0.6504 (m-10) cc_final: 0.6081 (m-10) REVERT: E 236 ARG cc_start: 0.7889 (ptt90) cc_final: 0.7431 (ptt180) REVERT: G 199 ASN cc_start: 0.9014 (t0) cc_final: 0.8592 (t0) REVERT: G 231 GLU cc_start: 0.8536 (pt0) cc_final: 0.8169 (pt0) REVERT: I 84 ASP cc_start: 0.8135 (t0) cc_final: 0.7690 (t0) REVERT: I 102 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7065 (p90) REVERT: I 152 GLN cc_start: 0.8426 (mm110) cc_final: 0.7962 (mm110) REVERT: I 241 MET cc_start: 0.7709 (mmm) cc_final: 0.7287 (mtp) REVERT: K 62 GLU cc_start: 0.8841 (mp0) cc_final: 0.8470 (mp0) REVERT: M 48 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8341 (mtt90) REVERT: M 50 GLU cc_start: 0.8232 (pm20) cc_final: 0.7803 (pm20) REVERT: O 19 LYS cc_start: 0.8396 (ptmt) cc_final: 0.8043 (ptmm) REVERT: O 59 MET cc_start: 0.7256 (ttt) cc_final: 0.6303 (ttp) REVERT: O 63 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8875 (mtmm) REVERT: O 73 ASP cc_start: 0.8160 (t0) cc_final: 0.7429 (t0) REVERT: P 80 ILE cc_start: 0.7218 (mt) cc_final: 0.6876 (mm) REVERT: F 76 GLN cc_start: 0.8779 (tp40) cc_final: 0.8510 (tm-30) REVERT: F 253 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8017 (ttp) REVERT: H 106 TYR cc_start: 0.8631 (p90) cc_final: 0.8402 (p90) REVERT: H 110 ASP cc_start: 0.9087 (t0) cc_final: 0.8784 (t0) REVERT: H 162 LYS cc_start: 0.8966 (mttt) cc_final: 0.8589 (mtpp) REVERT: H 183 MET cc_start: 0.8799 (ttm) cc_final: 0.8183 (ttm) REVERT: H 280 LYS cc_start: 0.8738 (tttt) cc_final: 0.8286 (tppt) REVERT: J 199 ASN cc_start: 0.9054 (t0) cc_final: 0.8541 (t0) REVERT: J 231 GLU cc_start: 0.8514 (pt0) cc_final: 0.8182 (pt0) REVERT: L 76 LYS cc_start: 0.8764 (mttt) cc_final: 0.8489 (mtpp) REVERT: L 102 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7067 (p90) REVERT: L 241 MET cc_start: 0.7703 (mmm) cc_final: 0.7296 (mtp) REVERT: N 68 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8709 (mmm160) REVERT: Q 48 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8459 (mtt90) REVERT: Q 50 GLU cc_start: 0.8230 (pm20) cc_final: 0.7822 (pm20) REVERT: Q 78 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7382 (tmtt) REVERT: R 19 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8017 (ptmm) REVERT: R 59 MET cc_start: 0.7280 (ttp) cc_final: 0.6875 (ttp) REVERT: R 63 LYS cc_start: 0.9283 (mtmm) cc_final: 0.8929 (mtmm) REVERT: R 73 ASP cc_start: 0.8203 (t0) cc_final: 0.7380 (t0) REVERT: S 25 SER cc_start: 0.8486 (m) cc_final: 0.8026 (p) REVERT: S 79 LYS cc_start: 0.6538 (mmmt) cc_final: 0.5921 (mmtm) outliers start: 99 outliers final: 81 residues processed: 661 average time/residue: 0.1732 time to fit residues: 175.9355 Evaluate side-chains 669 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 585 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 143 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 209 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 259 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 276 ASN G 152 GLN K 29 HIS K 97 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 118 GLN H 152 GLN H 227 ASN J 152 GLN N 97 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101021 restraints weight = 37440.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104758 restraints weight = 21398.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107190 restraints weight = 15055.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108778 restraints weight = 11993.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109819 restraints weight = 10320.023| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23238 Z= 0.193 Angle : 0.629 12.286 31754 Z= 0.318 Chirality : 0.046 0.176 3580 Planarity : 0.005 0.050 4038 Dihedral : 4.906 26.087 3096 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.06 % Allowed : 21.42 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 2826 helix: -2.33 (0.45), residues: 118 sheet: -0.77 (0.18), residues: 796 loop : -1.11 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 87 TYR 0.026 0.002 TYR D 106 PHE 0.027 0.002 PHE K 28 TRP 0.014 0.001 TRP E 171 HIS 0.005 0.001 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00466 (23234) covalent geometry : angle 0.62865 (31746) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.17462 ( 8) hydrogen bonds : bond 0.03739 ( 534) hydrogen bonds : angle 5.30939 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 586 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 MET cc_start: 0.7684 (ttp) cc_final: 0.7359 (tmm) REVERT: D 274 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8493 (mmtm) REVERT: E 110 ASP cc_start: 0.9130 (t0) cc_final: 0.8804 (t0) REVERT: E 162 LYS cc_start: 0.9036 (mttt) cc_final: 0.8620 (mtpp) REVERT: E 183 MET cc_start: 0.8747 (ttm) cc_final: 0.8103 (ttm) REVERT: E 206 ASP cc_start: 0.8799 (t70) cc_final: 0.8495 (t0) REVERT: E 222 TYR cc_start: 0.6383 (m-10) cc_final: 0.6049 (m-10) REVERT: E 278 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: G 199 ASN cc_start: 0.8974 (t0) cc_final: 0.8593 (t0) REVERT: G 231 GLU cc_start: 0.8526 (pt0) cc_final: 0.8166 (pt0) REVERT: I 102 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7178 (p90) REVERT: I 155 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8393 (tm-30) REVERT: I 241 MET cc_start: 0.7710 (mmm) cc_final: 0.7345 (mtp) REVERT: K 62 GLU cc_start: 0.8796 (mp0) cc_final: 0.8431 (mp0) REVERT: M 48 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8301 (mtt90) REVERT: M 50 GLU cc_start: 0.8292 (pm20) cc_final: 0.7884 (pm20) REVERT: O 19 LYS cc_start: 0.8414 (ptmt) cc_final: 0.8090 (ptmm) REVERT: O 59 MET cc_start: 0.7197 (ttt) cc_final: 0.6200 (ttp) REVERT: O 63 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8951 (mtmm) REVERT: P 80 ILE cc_start: 0.7291 (mt) cc_final: 0.6928 (mm) REVERT: F 230 MET cc_start: 0.7457 (ptp) cc_final: 0.7196 (ptp) REVERT: H 110 ASP cc_start: 0.9154 (t0) cc_final: 0.8834 (t0) REVERT: H 162 LYS cc_start: 0.8982 (mttt) cc_final: 0.8601 (mtpp) REVERT: H 183 MET cc_start: 0.8785 (ttm) cc_final: 0.8220 (ttm) REVERT: J 40 GLU cc_start: 0.8409 (tp30) cc_final: 0.8161 (tp30) REVERT: J 199 ASN cc_start: 0.9062 (t0) cc_final: 0.8520 (t0) REVERT: J 231 GLU cc_start: 0.8533 (pt0) cc_final: 0.8217 (pt0) REVERT: L 76 LYS cc_start: 0.8815 (mttt) cc_final: 0.8548 (mtpp) REVERT: L 102 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7038 (p90) REVERT: L 241 MET cc_start: 0.7711 (mmm) cc_final: 0.7339 (mtp) REVERT: N 68 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8757 (mmm160) REVERT: Q 14 LEU cc_start: 0.9037 (mt) cc_final: 0.8784 (tt) REVERT: Q 48 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8439 (mtt90) REVERT: Q 50 GLU cc_start: 0.8296 (pm20) cc_final: 0.7905 (pm20) REVERT: Q 78 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7370 (tmtt) REVERT: R 19 LYS cc_start: 0.8371 (ptmt) cc_final: 0.8046 (ptmm) REVERT: R 59 MET cc_start: 0.7339 (ttp) cc_final: 0.7003 (ttp) REVERT: R 63 LYS cc_start: 0.9289 (mtmm) cc_final: 0.8925 (mtmm) REVERT: S 25 SER cc_start: 0.8563 (m) cc_final: 0.7989 (p) REVERT: S 79 LYS cc_start: 0.6569 (mmmt) cc_final: 0.5946 (mmtm) outliers start: 101 outliers final: 84 residues processed: 654 average time/residue: 0.1740 time to fit residues: 175.1330 Evaluate side-chains 659 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 572 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 238 optimal weight: 0.9990 chunk 262 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN K 29 HIS ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 245 HIS ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN J 152 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098158 restraints weight = 37632.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101864 restraints weight = 21543.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104296 restraints weight = 15185.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105886 restraints weight = 12097.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106827 restraints weight = 10419.986| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23238 Z= 0.167 Angle : 0.620 13.427 31754 Z= 0.313 Chirality : 0.045 0.171 3580 Planarity : 0.005 0.064 4038 Dihedral : 4.841 25.785 3096 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.14 % Allowed : 21.66 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.15), residues: 2826 helix: -2.35 (0.46), residues: 116 sheet: -0.74 (0.18), residues: 786 loop : -1.07 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 236 TYR 0.026 0.002 TYR D 106 PHE 0.027 0.001 PHE K 28 TRP 0.023 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00405 (23234) covalent geometry : angle 0.62008 (31746) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.02306 ( 8) hydrogen bonds : bond 0.03596 ( 534) hydrogen bonds : angle 5.28400 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 584 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 MET cc_start: 0.7639 (ttp) cc_final: 0.7314 (tmm) REVERT: E 110 ASP cc_start: 0.9100 (t0) cc_final: 0.8754 (t0) REVERT: E 162 LYS cc_start: 0.9026 (mttt) cc_final: 0.8610 (mtpp) REVERT: E 183 MET cc_start: 0.8745 (ttm) cc_final: 0.8106 (ttm) REVERT: E 206 ASP cc_start: 0.8785 (t70) cc_final: 0.8471 (t0) REVERT: E 222 TYR cc_start: 0.6387 (m-10) cc_final: 0.6041 (m-10) REVERT: E 278 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8437 (m-40) REVERT: G 64 PHE cc_start: 0.9103 (m-80) cc_final: 0.8717 (m-80) REVERT: G 199 ASN cc_start: 0.8965 (t0) cc_final: 0.8595 (t0) REVERT: G 231 GLU cc_start: 0.8548 (pt0) cc_final: 0.8228 (pt0) REVERT: I 102 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7108 (p90) REVERT: I 155 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8402 (tm-30) REVERT: I 241 MET cc_start: 0.7697 (mmm) cc_final: 0.7360 (mtp) REVERT: K 62 GLU cc_start: 0.8761 (mp0) cc_final: 0.8405 (mp0) REVERT: K 231 ASP cc_start: 0.8686 (t0) cc_final: 0.8465 (t0) REVERT: M 48 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8298 (mtt90) REVERT: M 50 GLU cc_start: 0.8288 (pm20) cc_final: 0.7894 (pm20) REVERT: O 19 LYS cc_start: 0.8355 (ptmt) cc_final: 0.8025 (ptmm) REVERT: O 59 MET cc_start: 0.7259 (ttt) cc_final: 0.6374 (ttp) REVERT: O 63 LYS cc_start: 0.9311 (mtmt) cc_final: 0.8899 (mtmm) REVERT: P 4 MET cc_start: 0.9254 (mmm) cc_final: 0.8839 (mmm) REVERT: P 80 ILE cc_start: 0.7009 (mt) cc_final: 0.6580 (mm) REVERT: F 95 MET cc_start: 0.7529 (mmm) cc_final: 0.7005 (tpt) REVERT: F 230 MET cc_start: 0.7619 (ptp) cc_final: 0.7349 (ptp) REVERT: F 253 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8127 (ttp) REVERT: H 104 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7648 (t0) REVERT: H 110 ASP cc_start: 0.9133 (t0) cc_final: 0.8779 (t0) REVERT: H 118 GLN cc_start: 0.8402 (tp40) cc_final: 0.8059 (tt0) REVERT: H 162 LYS cc_start: 0.8980 (mttt) cc_final: 0.8603 (mtpp) REVERT: H 183 MET cc_start: 0.8795 (ttm) cc_final: 0.8236 (ttm) REVERT: J 40 GLU cc_start: 0.8436 (tp30) cc_final: 0.8193 (tp30) REVERT: J 199 ASN cc_start: 0.9009 (t0) cc_final: 0.8513 (t0) REVERT: J 231 GLU cc_start: 0.8508 (pt0) cc_final: 0.8186 (pt0) REVERT: L 76 LYS cc_start: 0.8770 (mttt) cc_final: 0.8506 (mtpp) REVERT: L 102 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.6970 (p90) REVERT: L 241 MET cc_start: 0.7705 (mmm) cc_final: 0.7383 (mtp) REVERT: N 231 ASP cc_start: 0.8625 (t0) cc_final: 0.8395 (t0) REVERT: Q 48 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8392 (mtt90) REVERT: Q 50 GLU cc_start: 0.8297 (pm20) cc_final: 0.7917 (pm20) REVERT: Q 78 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7380 (tmtt) REVERT: R 19 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8010 (ptmm) REVERT: R 59 MET cc_start: 0.7340 (ttp) cc_final: 0.7089 (ttp) REVERT: R 63 LYS cc_start: 0.9281 (mtmm) cc_final: 0.8906 (mtmm) REVERT: S 79 LYS cc_start: 0.6580 (mmmt) cc_final: 0.5936 (mmtm) outliers start: 103 outliers final: 84 residues processed: 650 average time/residue: 0.1704 time to fit residues: 171.6599 Evaluate side-chains 663 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 574 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 238 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN K 29 HIS ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN S 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112885 restraints weight = 36421.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116778 restraints weight = 20621.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119322 restraints weight = 14328.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120939 restraints weight = 11284.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122041 restraints weight = 9645.524| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23238 Z= 0.106 Angle : 0.588 13.123 31754 Z= 0.296 Chirality : 0.044 0.157 3580 Planarity : 0.004 0.048 4038 Dihedral : 4.499 23.993 3096 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.50 % Allowed : 22.27 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 2826 helix: -2.08 (0.46), residues: 118 sheet: -0.57 (0.18), residues: 772 loop : -0.96 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 236 TYR 0.026 0.001 TYR D 106 PHE 0.027 0.001 PHE K 28 TRP 0.019 0.001 TRP E 171 HIS 0.003 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00253 (23234) covalent geometry : angle 0.58825 (31746) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.78219 ( 8) hydrogen bonds : bond 0.03161 ( 534) hydrogen bonds : angle 5.10571 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4785.77 seconds wall clock time: 83 minutes 14.15 seconds (4994.15 seconds total)