Starting phenix.real_space_refine on Fri Jan 24 18:25:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9b_38171/01_2025/8x9b_38171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9b_38171/01_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_38171/01_2025/8x9b_38171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9b_38171/01_2025/8x9b_38171.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9b_38171/01_2025/8x9b_38171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9b_38171/01_2025/8x9b_38171.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: H, S, R, F, J, L, Q, N Time building chain proxies: 12.75, per 1000 atoms: 0.56 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=2, 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 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: 5.08 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.18 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: 8.07 Time building geometry restraints manager: 5.95 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: 808 34.60 - 51.90: 120 51.90 - 69.20: 36 69.20 - 86.50: 20 Dihedral angle restraints: 13650 sinusoidal: 5280 harmonic: 8370 Sorted by residual: 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 dihedral pdb=" N PHE J 82 " pdb=" C PHE J 82 " pdb=" CA PHE J 82 " pdb=" CB PHE J 82 " ideal model delta harmonic sigma weight residual 122.80 133.57 -10.77 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 13647 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: 2.03 - 2.60: 350 2.60 - 3.18: 18318 3.18 - 3.75: 31514 3.75 - 4.33: 43271 4.33 - 4.90: 73984 Nonbonded interactions: 167437 Sorted by model distance: nonbonded pdb=" SG CYS R 22 " pdb=" SG CYS R 96 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS S 23 " pdb=" SG CYS S 93 " model vdw 2.061 3.760 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 ... (remaining 167432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'N' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 47.460 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- 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 23234 Z= 0.783 Angle : 1.572 16.548 31746 Z= 1.020 Chirality : 0.100 0.681 3580 Planarity : 0.011 0.148 4038 Dihedral : 12.253 86.504 8260 Min Nonbonded Distance : 2.028 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP S 40 HIS 0.006 0.001 HIS I 118 PHE 0.024 0.003 PHE D 84 TYR 0.022 0.003 TYR N 107 ARG 0.017 0.002 ARG F 130 *********************** 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 : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.3902 time to fit residues: 592.1768 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 : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 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 O 57 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 ASN R 57 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 = 0.3632 r_free = 0.3632 target = 0.139106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110062 restraints weight = 36993.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113889 restraints weight = 20451.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116393 restraints weight = 14057.159| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23234 Z= 0.281 Angle : 0.673 10.104 31746 Z= 0.349 Chirality : 0.048 0.192 3580 Planarity : 0.006 0.063 4038 Dihedral : 5.145 27.949 3096 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.58 % Allowed : 13.83 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 2826 helix: -3.42 (0.32), residues: 122 sheet: -1.14 (0.17), residues: 808 loop : -1.67 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 171 HIS 0.006 0.001 HIS I 145 PHE 0.025 0.002 PHE R 27 TYR 0.026 0.002 TYR P 92 ARG 0.008 0.001 ARG M 68 *********************** 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 805 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 716 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8893 (tp40) cc_final: 0.8593 (tp-100) REVERT: D 143 ASN cc_start: 0.8898 (p0) cc_final: 0.8451 (p0) REVERT: D 205 TYR cc_start: 0.8121 (t80) cc_final: 0.7831 (t80) REVERT: D 278 ASN cc_start: 0.8485 (m110) cc_final: 0.8278 (m110) REVERT: D 279 TYR cc_start: 0.8722 (p90) cc_final: 0.8279 (p90) REVERT: E 106 TYR cc_start: 0.8634 (p90) cc_final: 0.8387 (p90) REVERT: E 119 LEU cc_start: 0.8771 (tp) cc_final: 0.8548 (tp) REVERT: E 147 VAL cc_start: 0.8465 (t) cc_final: 0.7954 (p) REVERT: E 149 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7790 (tp40) REVERT: E 183 MET cc_start: 0.8899 (ttm) cc_final: 0.8392 (ttm) REVERT: G 30 ASN cc_start: 0.8047 (m-40) cc_final: 0.7789 (t0) REVERT: G 62 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7166 (mmm160) REVERT: G 74 ASP cc_start: 0.7374 (p0) cc_final: 0.7134 (p0) REVERT: G 104 SER cc_start: 0.8981 (t) cc_final: 0.8706 (m) REVERT: G 127 LEU cc_start: 0.8421 (tp) cc_final: 0.8074 (tp) REVERT: G 130 TYR cc_start: 0.8844 (t80) cc_final: 0.8547 (t80) REVERT: G 164 TYR cc_start: 0.9175 (t80) cc_final: 0.8848 (t80) REVERT: G 199 ASN cc_start: 0.8953 (t0) cc_final: 0.8652 (t0) REVERT: G 231 GLU cc_start: 0.8500 (pt0) cc_final: 0.8256 (pt0) REVERT: I 30 ASN cc_start: 0.7331 (m-40) cc_final: 0.7002 (p0) REVERT: I 76 LYS cc_start: 0.8910 (mttt) cc_final: 0.8688 (mtpp) REVERT: I 209 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8372 (t70) REVERT: I 223 ASP cc_start: 0.8614 (t0) cc_final: 0.8368 (m-30) REVERT: K 28 PHE cc_start: 0.8143 (t80) cc_final: 0.7815 (t80) REVERT: K 78 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8495 (mmmt) REVERT: K 226 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: M 74 SER cc_start: 0.8689 (t) cc_final: 0.8480 (p) REVERT: O 3 GLN cc_start: 0.7682 (pt0) cc_final: 0.7438 (pm20) REVERT: O 19 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7881 (ptmm) REVERT: P 97 THR cc_start: 0.8735 (m) cc_final: 0.8449 (p) REVERT: F 76 GLN cc_start: 0.8819 (tp40) cc_final: 0.8476 (tp-100) REVERT: F 143 ASN cc_start: 0.8792 (p0) cc_final: 0.8465 (p0) REVERT: F 205 TYR cc_start: 0.8151 (t80) cc_final: 0.7834 (t80) REVERT: F 279 TYR cc_start: 0.8838 (p90) cc_final: 0.8617 (p90) REVERT: H 147 VAL cc_start: 0.8409 (t) cc_final: 0.7991 (p) REVERT: H 183 MET cc_start: 0.8976 (ttm) cc_final: 0.8349 (ttm) REVERT: J 127 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8236 (tp) REVERT: J 164 TYR cc_start: 0.9195 (t80) cc_final: 0.8932 (t80) REVERT: J 199 ASN cc_start: 0.9011 (t0) cc_final: 0.8673 (t0) REVERT: J 231 GLU cc_start: 0.8428 (pt0) cc_final: 0.8195 (pt0) REVERT: L 30 ASN cc_start: 0.7358 (m-40) cc_final: 0.7050 (p0) REVERT: L 76 LYS cc_start: 0.8873 (mttt) cc_final: 0.8610 (mtpp) REVERT: L 84 ASP cc_start: 0.8094 (t70) cc_final: 0.7816 (t0) REVERT: Q 78 LYS cc_start: 0.7877 (tmtt) cc_final: 0.7576 (tmtt) REVERT: R 3 GLN cc_start: 0.7655 (pt0) cc_final: 0.7453 (pm20) REVERT: R 19 LYS cc_start: 0.8183 (ptmt) cc_final: 0.7836 (ptmm) REVERT: S 54 TYR cc_start: 0.7212 (t80) cc_final: 0.7002 (t80) REVERT: S 80 ILE cc_start: 0.7299 (mt) cc_final: 0.7078 (mm) REVERT: S 95 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7670 (tm-30) outliers start: 89 outliers final: 54 residues processed: 757 average time/residue: 0.3512 time to fit residues: 405.3780 Evaluate side-chains 700 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 642 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR 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 132 LEU 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 I residue 40 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 99 THR 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 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 98 ARG 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 247 ILE 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 115 SER Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 116 GLU 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 58 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 95 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 211 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN I 145 HIS I 208 ASN I 209 HIS K 12 GLN K 29 HIS ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN O 43 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 H 118 GLN H 227 ASN H 276 ASN J 152 GLN J 211 ASN L 145 HIS L 209 HIS ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 GLN Q 199 GLN R 43 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111574 restraints weight = 36650.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115429 restraints weight = 20228.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117972 restraints weight = 13894.085| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23234 Z= 0.172 Angle : 0.591 8.737 31746 Z= 0.300 Chirality : 0.045 0.215 3580 Planarity : 0.005 0.054 4038 Dihedral : 4.740 26.291 3096 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.22 % Allowed : 16.16 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 2826 helix: -3.19 (0.36), residues: 120 sheet: -0.84 (0.17), residues: 836 loop : -1.32 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 171 HIS 0.008 0.001 HIS I 209 PHE 0.025 0.001 PHE O 27 TYR 0.020 0.001 TYR H 106 ARG 0.005 0.001 ARG H 236 *********************** 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 785 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 680 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8624 (tp40) cc_final: 0.7940 (tm-30) REVERT: D 82 ASN cc_start: 0.8743 (m110) cc_final: 0.7944 (m-40) REVERT: D 185 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7813 (t0) REVERT: D 279 TYR cc_start: 0.8642 (p90) cc_final: 0.8282 (p90) REVERT: E 147 VAL cc_start: 0.8647 (t) cc_final: 0.8392 (p) REVERT: E 162 LYS cc_start: 0.8731 (mttm) cc_final: 0.8447 (mtpp) REVERT: E 183 MET cc_start: 0.8974 (ttm) cc_final: 0.8662 (ttm) REVERT: G 74 ASP cc_start: 0.7428 (p0) cc_final: 0.7221 (p0) REVERT: G 104 SER cc_start: 0.8984 (t) cc_final: 0.8561 (m) REVERT: G 127 LEU cc_start: 0.8469 (tp) cc_final: 0.8129 (tp) REVERT: G 199 ASN cc_start: 0.9060 (t0) cc_final: 0.8612 (t0) REVERT: G 231 GLU cc_start: 0.8436 (pt0) cc_final: 0.8175 (pt0) REVERT: I 84 ASP cc_start: 0.8050 (t0) cc_final: 0.7828 (t0) REVERT: K 78 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8650 (mmmt) REVERT: K 226 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7684 (mtt) REVERT: O 3 GLN cc_start: 0.7661 (pt0) cc_final: 0.7447 (pm20) REVERT: O 19 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7890 (ptmm) REVERT: O 63 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8912 (mtmm) REVERT: P 54 TYR cc_start: 0.7096 (t80) cc_final: 0.6595 (t80) REVERT: F 76 GLN cc_start: 0.8824 (tp40) cc_final: 0.8586 (tp-100) REVERT: F 185 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (t0) REVERT: H 149 GLN cc_start: 0.8356 (tp40) cc_final: 0.7977 (tp40) REVERT: H 162 LYS cc_start: 0.8770 (mttm) cc_final: 0.8500 (mtpp) REVERT: H 183 MET cc_start: 0.8942 (ttm) cc_final: 0.8681 (ttm) REVERT: H 275 THR cc_start: 0.8845 (p) cc_final: 0.8573 (t) REVERT: J 74 ASP cc_start: 0.7449 (p0) cc_final: 0.7178 (p0) REVERT: J 79 TYR cc_start: 0.8866 (p90) cc_final: 0.8626 (p90) REVERT: J 81 LYS cc_start: 0.8754 (mttm) cc_final: 0.8516 (mttm) REVERT: J 127 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8278 (tp) REVERT: J 199 ASN cc_start: 0.9074 (t0) cc_final: 0.8571 (t0) REVERT: J 231 GLU cc_start: 0.8384 (pt0) cc_final: 0.8137 (pt0) REVERT: L 76 LYS cc_start: 0.8759 (mttt) cc_final: 0.8517 (mtpp) REVERT: L 84 ASP cc_start: 0.8087 (t70) cc_final: 0.7822 (t0) REVERT: Q 48 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8187 (mtt-85) REVERT: R 19 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7863 (ptmm) REVERT: R 63 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8922 (mtmm) outliers start: 105 outliers final: 78 residues processed: 733 average time/residue: 0.3601 time to fit residues: 402.1244 Evaluate side-chains 716 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 634 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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 272 LEU 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 225 CYS 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 235 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 139 THR 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 99 THR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 226 MET 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 O residue 71 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 52 LEU 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 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 225 CYS Chi-restraints excluded: chain H residue 232 THR 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 173 SER 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 50 GLU 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 38 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 163 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 227 ASN J 152 GLN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 HIS L 208 ASN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103957 restraints weight = 38326.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107515 restraints weight = 22188.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109849 restraints weight = 15673.215| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 23234 Z= 0.486 Angle : 0.738 10.415 31746 Z= 0.379 Chirality : 0.049 0.196 3580 Planarity : 0.006 0.078 4038 Dihedral : 5.407 27.940 3096 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.83 % Allowed : 17.00 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 2826 helix: -2.99 (0.36), residues: 122 sheet: -0.95 (0.17), residues: 830 loop : -1.44 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 171 HIS 0.006 0.001 HIS R 35 PHE 0.029 0.003 PHE K 28 TYR 0.024 0.003 TYR R 95 ARG 0.019 0.001 ARG E 236 *********************** 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 792 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 647 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8728 (tp40) cc_final: 0.8294 (tm-30) REVERT: D 82 ASN cc_start: 0.8923 (m110) cc_final: 0.8630 (m-40) REVERT: D 95 MET cc_start: 0.7792 (ttp) cc_final: 0.7540 (tmm) REVERT: E 110 ASP cc_start: 0.9051 (t0) cc_final: 0.8817 (t0) REVERT: E 147 VAL cc_start: 0.8630 (t) cc_final: 0.8423 (p) REVERT: E 149 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8293 (tp-100) REVERT: G 79 TYR cc_start: 0.9006 (p90) cc_final: 0.8741 (p90) REVERT: G 199 ASN cc_start: 0.9094 (t0) cc_final: 0.8708 (t0) REVERT: I 241 MET cc_start: 0.8046 (mmm) cc_final: 0.7590 (mtp) REVERT: K 78 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8749 (mmmt) REVERT: K 226 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: K 231 ASP cc_start: 0.8758 (t70) cc_final: 0.8371 (t0) REVERT: O 3 GLN cc_start: 0.7990 (pt0) cc_final: 0.7726 (pm20) REVERT: O 19 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8045 (ptmm) REVERT: O 63 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8902 (mtmm) REVERT: P 80 ILE cc_start: 0.7509 (mt) cc_final: 0.7199 (mm) REVERT: F 76 GLN cc_start: 0.8906 (tp40) cc_final: 0.8609 (tm-30) REVERT: F 195 MET cc_start: 0.7227 (mmm) cc_final: 0.6783 (mmm) REVERT: H 110 ASP cc_start: 0.9032 (t0) cc_final: 0.8814 (t0) REVERT: H 118 GLN cc_start: 0.8862 (tp40) cc_final: 0.8587 (tp-100) REVERT: H 149 GLN cc_start: 0.8563 (tp40) cc_final: 0.8264 (tp-100) REVERT: J 30 ASN cc_start: 0.8315 (m-40) cc_final: 0.7988 (t0) REVERT: J 82 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6779 (t80) REVERT: J 199 ASN cc_start: 0.9077 (t0) cc_final: 0.8552 (t0) REVERT: J 231 GLU cc_start: 0.8546 (pt0) cc_final: 0.8308 (pt0) REVERT: L 76 LYS cc_start: 0.8955 (mttt) cc_final: 0.8753 (mtpp) REVERT: L 84 ASP cc_start: 0.8338 (t70) cc_final: 0.8078 (t0) REVERT: L 223 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: N 28 PHE cc_start: 0.8060 (t80) cc_final: 0.7779 (t80) REVERT: N 231 ASP cc_start: 0.8770 (t70) cc_final: 0.8535 (t0) REVERT: R 19 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8107 (ptmm) REVERT: R 22 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8404 (p) REVERT: R 63 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8906 (mtmm) REVERT: S 79 LYS cc_start: 0.6494 (mmmt) cc_final: 0.6231 (tttm) REVERT: S 80 ILE cc_start: 0.7372 (mt) cc_final: 0.7079 (mt) outliers start: 145 outliers final: 111 residues processed: 727 average time/residue: 0.3471 time to fit residues: 388.4965 Evaluate side-chains 720 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 605 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 176 ASN 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 151 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 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 139 THR Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 226 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 64 THR 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 164 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 71 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 111 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 247 ILE 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 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 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 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 82 PHE Chi-restraints excluded: chain J residue 85 VAL 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 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 223 ASP Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 64 THR 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 204 VAL Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 71 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 174 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 161 optimal weight: 0.0000 chunk 280 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 245 HIS E 227 ASN G 109 HIS G 152 GLN K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN F 245 HIS H 227 ASN J 152 GLN L 155 GLN L 209 HIS N 67 GLN N 97 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109549 restraints weight = 37464.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113280 restraints weight = 21173.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115753 restraints weight = 14748.854| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23234 Z= 0.151 Angle : 0.574 8.981 31746 Z= 0.290 Chirality : 0.044 0.174 3580 Planarity : 0.005 0.049 4038 Dihedral : 4.737 24.947 3096 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.78 % Allowed : 20.02 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 2826 helix: -2.78 (0.38), residues: 122 sheet: -0.67 (0.17), residues: 822 loop : -1.12 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 171 HIS 0.004 0.001 HIS G 162 PHE 0.023 0.001 PHE H 273 TYR 0.025 0.001 TYR F 106 ARG 0.007 0.001 ARG P 58 *********************** 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 734 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 640 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8680 (tp40) cc_final: 0.8378 (tm-30) REVERT: D 82 ASN cc_start: 0.8920 (m110) cc_final: 0.8703 (m-40) REVERT: D 253 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: E 147 VAL cc_start: 0.8565 (t) cc_final: 0.8050 (p) REVERT: E 149 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8246 (tp-100) REVERT: E 183 MET cc_start: 0.8837 (ttm) cc_final: 0.8517 (ttm) REVERT: E 206 ASP cc_start: 0.8581 (t70) cc_final: 0.8125 (t0) REVERT: E 222 TYR cc_start: 0.6403 (m-80) cc_final: 0.6104 (m-80) REVERT: E 253 MET cc_start: 0.8216 (ttm) cc_final: 0.7812 (ttp) REVERT: E 280 LYS cc_start: 0.8675 (tttt) cc_final: 0.8338 (tppt) REVERT: G 199 ASN cc_start: 0.9112 (t0) cc_final: 0.8656 (t0) REVERT: I 84 ASP cc_start: 0.8007 (t0) cc_final: 0.7607 (t0) REVERT: I 100 TYR cc_start: 0.6444 (t80) cc_final: 0.6186 (t80) REVERT: I 152 GLN cc_start: 0.8461 (mm110) cc_final: 0.8032 (mm110) REVERT: I 241 MET cc_start: 0.7934 (mmm) cc_final: 0.7402 (mtp) REVERT: K 226 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7601 (mtp) REVERT: O 19 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7954 (ptmm) REVERT: O 63 LYS cc_start: 0.9253 (mtmt) cc_final: 0.8918 (mtmm) REVERT: P 80 ILE cc_start: 0.7120 (mt) cc_final: 0.6819 (mm) REVERT: F 76 GLN cc_start: 0.8750 (tp40) cc_final: 0.8369 (tm-30) REVERT: F 82 ASN cc_start: 0.8850 (m110) cc_final: 0.8650 (m-40) REVERT: F 195 MET cc_start: 0.7012 (mmm) cc_final: 0.6572 (mmm) REVERT: F 253 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8001 (ttp) REVERT: H 110 ASP cc_start: 0.8965 (t0) cc_final: 0.8754 (t0) REVERT: H 183 MET cc_start: 0.8782 (ttm) cc_final: 0.8273 (ttm) REVERT: H 280 LYS cc_start: 0.8560 (tttt) cc_final: 0.8211 (tppt) REVERT: J 30 ASN cc_start: 0.8097 (m-40) cc_final: 0.7869 (t0) REVERT: J 81 LYS cc_start: 0.8863 (mttm) cc_final: 0.8620 (mttm) REVERT: J 199 ASN cc_start: 0.9131 (t0) cc_final: 0.8633 (t0) REVERT: J 231 GLU cc_start: 0.8435 (pt0) cc_final: 0.8199 (pt0) REVERT: L 76 LYS cc_start: 0.8695 (mttt) cc_final: 0.8437 (mtpp) REVERT: L 84 ASP cc_start: 0.8154 (t70) cc_final: 0.7944 (t0) REVERT: L 241 MET cc_start: 0.7950 (mmm) cc_final: 0.7409 (mtp) REVERT: N 14 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9048 (tp) REVERT: N 78 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8308 (mmtm) REVERT: R 19 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7856 (ptmm) REVERT: R 22 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8532 (p) REVERT: R 63 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8958 (mtmm) REVERT: R 95 TYR cc_start: 0.8648 (m-80) cc_final: 0.8432 (m-80) REVERT: S 79 LYS cc_start: 0.6305 (mmmt) cc_final: 0.5962 (tttm) REVERT: S 80 ILE cc_start: 0.7013 (mt) cc_final: 0.6624 (mm) outliers start: 94 outliers final: 55 residues processed: 692 average time/residue: 0.3546 time to fit residues: 374.8309 Evaluate side-chains 666 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 606 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 272 LEU 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 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 CYS 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 231 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 226 MET Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 215 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 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 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 73 LYS Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 152 GLN Chi-restraints excluded: chain J residue 170 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 115 SER Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 225 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS 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 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 28 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 149 GLN E 227 ASN G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 245 HIS H 227 ASN J 109 HIS J 152 GLN N 67 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105383 restraints weight = 37725.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109032 restraints weight = 21582.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111438 restraints weight = 15129.848| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23234 Z= 0.305 Angle : 0.615 10.302 31746 Z= 0.310 Chirality : 0.046 0.207 3580 Planarity : 0.005 0.051 4038 Dihedral : 4.806 25.380 3096 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.86 % Allowed : 19.86 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 2826 helix: -2.48 (0.41), residues: 122 sheet: -0.68 (0.18), residues: 806 loop : -1.13 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 171 HIS 0.004 0.001 HIS I 109 PHE 0.033 0.002 PHE N 28 TYR 0.025 0.002 TYR S 54 ARG 0.007 0.000 ARG N 68 *********************** 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 723 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 602 time to evaluate : 2.562 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: 0.8682 (tp40) cc_final: 0.8398 (tm-30) REVERT: E 147 VAL cc_start: 0.8552 (t) cc_final: 0.8149 (p) REVERT: E 149 GLN cc_start: 0.8534 (tp40) cc_final: 0.8311 (tp-100) REVERT: E 183 MET cc_start: 0.8901 (ttm) cc_final: 0.8540 (ttm) REVERT: E 206 ASP cc_start: 0.8612 (t70) cc_final: 0.8286 (t0) REVERT: E 222 TYR cc_start: 0.6454 (m-80) cc_final: 0.6031 (m-80) REVERT: G 199 ASN cc_start: 0.9104 (t0) cc_final: 0.8639 (t0) REVERT: I 102 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6973 (p90) REVERT: I 165 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8981 (m) REVERT: I 241 MET cc_start: 0.7962 (mmm) cc_final: 0.7412 (mtp) REVERT: K 226 MET cc_start: 0.8026 (mtt) cc_final: 0.7702 (mtp) REVERT: M 48 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8304 (mtt90) REVERT: O 19 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7993 (ptmm) REVERT: O 59 MET cc_start: 0.7004 (ttp) cc_final: 0.6416 (ttp) REVERT: O 63 LYS cc_start: 0.9262 (mtmt) cc_final: 0.8888 (mtmm) REVERT: P 24 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7744 (ttpp) REVERT: P 42 GLN cc_start: 0.8329 (tt0) cc_final: 0.8046 (tt0) REVERT: P 80 ILE cc_start: 0.7300 (mt) cc_final: 0.6933 (mm) REVERT: F 76 GLN cc_start: 0.8740 (tp40) cc_final: 0.8476 (tm-30) REVERT: H 110 ASP cc_start: 0.9097 (t0) cc_final: 0.8881 (t0) REVERT: H 149 GLN cc_start: 0.8613 (tp40) cc_final: 0.8349 (tp40) REVERT: H 183 MET cc_start: 0.8821 (ttm) cc_final: 0.8292 (ttm) REVERT: H 206 ASP cc_start: 0.8637 (t70) cc_final: 0.8249 (t0) REVERT: H 280 LYS cc_start: 0.8650 (tttt) cc_final: 0.8280 (tppt) REVERT: J 30 ASN cc_start: 0.8275 (m-40) cc_final: 0.7989 (t0) REVERT: J 197 TYR cc_start: 0.8629 (t80) cc_final: 0.8267 (t80) REVERT: J 199 ASN cc_start: 0.9114 (t0) cc_final: 0.8474 (t0) REVERT: J 231 GLU cc_start: 0.8489 (pt0) cc_final: 0.8243 (pt0) REVERT: L 76 LYS cc_start: 0.8821 (mttt) cc_final: 0.8619 (mtpp) REVERT: L 84 ASP cc_start: 0.8269 (t70) cc_final: 0.8012 (t0) REVERT: L 102 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7099 (p90) REVERT: L 241 MET cc_start: 0.7963 (mmm) cc_final: 0.7445 (mtp) REVERT: N 14 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9127 (tp) REVERT: Q 48 ARG cc_start: 0.8637 (mtt90) cc_final: 0.8357 (mtt90) REVERT: R 19 LYS cc_start: 0.8363 (ptmt) cc_final: 0.8079 (ptmt) REVERT: R 22 CYS cc_start: 0.8871 (p) cc_final: 0.8526 (p) REVERT: R 63 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8941 (mtmm) REVERT: S 79 LYS cc_start: 0.6379 (mmmt) cc_final: 0.6019 (tttm) REVERT: S 80 ILE cc_start: 0.7326 (mt) cc_final: 0.6954 (mm) outliers start: 121 outliers final: 87 residues processed: 674 average time/residue: 0.3636 time to fit residues: 373.8238 Evaluate side-chains 681 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 590 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 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 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 170 ILE 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 230 SER 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 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 165 VAL 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 M residue 21 SER Chi-restraints excluded: chain M residue 34 ILE 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 105 CYS 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 71 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 98 ARG 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 156 VAL Chi-restraints excluded: chain F residue 176 ASN 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 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 73 LYS 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 N residue 14 LEU 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 164 SER 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 R residue 58 THR Chi-restraints excluded: chain R residue 71 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 52 LEU Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 103 optimal weight: 6.9990 chunk 150 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 251 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 161 optimal weight: 0.0070 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.8378 ------------------------------------------------------------------------------- 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** E 227 ASN G 152 GLN G 225 ASN K 97 GLN P 6 GLN P 43 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 J 225 ASN L 155 GLN N 97 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109790 restraints weight = 37384.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113504 restraints weight = 21015.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115972 restraints weight = 14577.633| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23234 Z= 0.151 Angle : 0.566 10.919 31746 Z= 0.284 Chirality : 0.044 0.175 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.492 23.480 3096 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.98 % Allowed : 20.82 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2826 helix: -2.27 (0.44), residues: 122 sheet: -0.49 (0.18), residues: 796 loop : -0.96 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 171 HIS 0.003 0.001 HIS L 109 PHE 0.023 0.001 PHE N 28 TYR 0.026 0.001 TYR F 106 ARG 0.006 0.000 ARG R 87 *********************** 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 727 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 628 time to evaluate : 2.739 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: E 147 VAL cc_start: 0.8553 (t) cc_final: 0.8152 (p) REVERT: E 183 MET cc_start: 0.8839 (ttm) cc_final: 0.8493 (ttm) REVERT: E 206 ASP cc_start: 0.8671 (t70) cc_final: 0.8273 (t0) REVERT: E 222 TYR cc_start: 0.6416 (m-80) cc_final: 0.6016 (m-80) REVERT: E 276 ASN cc_start: 0.8681 (p0) cc_final: 0.8402 (p0) REVERT: E 278 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8433 (m-40) REVERT: E 280 LYS cc_start: 0.8681 (tttt) cc_final: 0.8307 (tppt) REVERT: G 64 PHE cc_start: 0.9090 (m-80) cc_final: 0.8733 (m-80) REVERT: G 199 ASN cc_start: 0.9098 (t0) cc_final: 0.8599 (t0) REVERT: I 100 TYR cc_start: 0.6493 (t80) cc_final: 0.6200 (t80) REVERT: I 241 MET cc_start: 0.7833 (mmm) cc_final: 0.7282 (mtp) REVERT: K 226 MET cc_start: 0.7995 (mtt) cc_final: 0.7762 (mtp) REVERT: O 19 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7939 (ptmm) REVERT: O 59 MET cc_start: 0.7224 (ttp) cc_final: 0.6769 (ttp) REVERT: O 63 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8916 (mtmm) REVERT: P 4 MET cc_start: 0.9177 (mmm) cc_final: 0.8969 (mmm) REVERT: P 24 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7701 (ttpp) REVERT: P 54 TYR cc_start: 0.6906 (t80) cc_final: 0.6652 (t80) REVERT: P 80 ILE cc_start: 0.7036 (mt) cc_final: 0.6696 (mm) REVERT: F 76 GLN cc_start: 0.8646 (tp40) cc_final: 0.8443 (tm-30) REVERT: F 253 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: H 107 VAL cc_start: 0.8988 (t) cc_final: 0.8608 (m) REVERT: H 110 ASP cc_start: 0.8942 (t0) cc_final: 0.8710 (t0) REVERT: H 176 ASN cc_start: 0.8882 (m-40) cc_final: 0.8502 (p0) REVERT: H 183 MET cc_start: 0.8767 (ttm) cc_final: 0.8235 (ttm) REVERT: H 280 LYS cc_start: 0.8630 (tttt) cc_final: 0.8272 (tppt) REVERT: J 30 ASN cc_start: 0.8149 (m-40) cc_final: 0.7929 (t0) REVERT: J 81 LYS cc_start: 0.8863 (mttm) cc_final: 0.8577 (mmmm) REVERT: J 197 TYR cc_start: 0.8591 (t80) cc_final: 0.8315 (t80) REVERT: J 199 ASN cc_start: 0.9094 (t0) cc_final: 0.8457 (t0) REVERT: J 231 GLU cc_start: 0.8493 (pt0) cc_final: 0.8133 (pt0) REVERT: L 76 LYS cc_start: 0.8670 (mttt) cc_final: 0.8459 (mtpp) REVERT: L 84 ASP cc_start: 0.8180 (t70) cc_final: 0.7926 (t0) REVERT: L 241 MET cc_start: 0.7851 (mmm) cc_final: 0.7332 (mtp) REVERT: R 19 LYS cc_start: 0.8259 (ptmt) cc_final: 0.8005 (ptmt) REVERT: R 22 CYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8538 (p) REVERT: R 59 MET cc_start: 0.6988 (ttp) cc_final: 0.6687 (ttp) REVERT: R 63 LYS cc_start: 0.9244 (mtmt) cc_final: 0.8947 (mtmm) REVERT: R 73 ASP cc_start: 0.8045 (t0) cc_final: 0.7303 (t0) REVERT: S 79 LYS cc_start: 0.6383 (mmmt) cc_final: 0.5753 (mmtm) REVERT: S 80 ILE cc_start: 0.7087 (mt) cc_final: 0.6703 (mm) outliers start: 99 outliers final: 66 residues processed: 688 average time/residue: 0.3761 time to fit residues: 394.4892 Evaluate side-chains 680 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 611 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 77 GLU 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 272 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 192 VAL 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 I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 164 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 105 CYS 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 98 ARG 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 156 VAL 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 272 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL 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 201 VAL Chi-restraints excluded: chain J residue 230 SER 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 N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS 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 Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 227 ASN G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN F 82 ASN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 227 ASN J 109 HIS J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN S 43 GLN S 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111578 restraints weight = 36888.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115421 restraints weight = 20675.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117951 restraints weight = 14394.927| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23234 Z= 0.189 Angle : 0.576 11.731 31746 Z= 0.288 Chirality : 0.044 0.243 3580 Planarity : 0.004 0.051 4038 Dihedral : 4.440 24.890 3096 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.78 % Allowed : 21.42 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 2826 helix: -2.03 (0.46), residues: 122 sheet: -0.54 (0.18), residues: 810 loop : -0.89 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 203 HIS 0.003 0.001 HIS L 109 PHE 0.027 0.001 PHE O 27 TYR 0.025 0.001 TYR F 106 ARG 0.006 0.000 ARG R 87 *********************** 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 705 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 611 time to evaluate : 2.673 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: E 147 VAL cc_start: 0.8633 (t) cc_final: 0.8163 (p) REVERT: E 183 MET cc_start: 0.8777 (ttm) cc_final: 0.8469 (ttm) REVERT: E 206 ASP cc_start: 0.8682 (t70) cc_final: 0.8319 (t0) REVERT: E 222 TYR cc_start: 0.6430 (m-80) cc_final: 0.5876 (m-80) REVERT: E 276 ASN cc_start: 0.8670 (p0) cc_final: 0.8413 (p0) REVERT: E 278 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: G 64 PHE cc_start: 0.9141 (m-80) cc_final: 0.8809 (m-80) REVERT: G 199 ASN cc_start: 0.9071 (t0) cc_final: 0.8533 (t0) REVERT: G 231 GLU cc_start: 0.8543 (pt0) cc_final: 0.8166 (pt0) REVERT: I 102 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6875 (p90) REVERT: I 241 MET cc_start: 0.7779 (mmm) cc_final: 0.7258 (mtp) REVERT: K 231 ASP cc_start: 0.8876 (t0) cc_final: 0.8660 (t0) REVERT: M 224 PHE cc_start: 0.9034 (t80) cc_final: 0.8658 (t80) REVERT: O 19 LYS cc_start: 0.8359 (ptmt) cc_final: 0.8016 (ptmm) REVERT: O 59 MET cc_start: 0.7124 (ttp) cc_final: 0.6428 (ttp) REVERT: O 63 LYS cc_start: 0.9270 (mtmt) cc_final: 0.8911 (mtmm) REVERT: O 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7303 (t0) REVERT: P 24 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7791 (ttpp) REVERT: P 42 GLN cc_start: 0.8313 (tt0) cc_final: 0.8076 (tt0) REVERT: P 80 ILE cc_start: 0.7061 (mt) cc_final: 0.6705 (mm) REVERT: F 95 MET cc_start: 0.7640 (mmm) cc_final: 0.7103 (tpt) REVERT: F 253 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7896 (ttp) REVERT: H 110 ASP cc_start: 0.8921 (t0) cc_final: 0.8680 (t0) REVERT: H 176 ASN cc_start: 0.8882 (m-40) cc_final: 0.8561 (p0) REVERT: H 183 MET cc_start: 0.8747 (ttm) cc_final: 0.8217 (ttm) REVERT: H 280 LYS cc_start: 0.8633 (tttt) cc_final: 0.8277 (tppt) REVERT: J 30 ASN cc_start: 0.8146 (m-40) cc_final: 0.7899 (t0) REVERT: J 197 TYR cc_start: 0.8639 (t80) cc_final: 0.8366 (t80) REVERT: J 199 ASN cc_start: 0.9067 (t0) cc_final: 0.8439 (t0) REVERT: J 231 GLU cc_start: 0.8493 (pt0) cc_final: 0.8158 (pt0) REVERT: L 84 ASP cc_start: 0.8076 (t70) cc_final: 0.7847 (t0) REVERT: L 100 TYR cc_start: 0.6124 (t80) cc_final: 0.5897 (t80) REVERT: L 102 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6822 (p90) REVERT: L 241 MET cc_start: 0.7793 (mmm) cc_final: 0.7289 (mtp) REVERT: N 92 ARG cc_start: 0.8671 (ptp-110) cc_final: 0.8038 (mtp85) REVERT: Q 48 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8142 (mmt90) REVERT: R 19 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8103 (ptmt) REVERT: R 22 CYS cc_start: 0.8867 (p) cc_final: 0.8507 (p) REVERT: R 59 MET cc_start: 0.7093 (ttp) cc_final: 0.6834 (ttp) REVERT: R 63 LYS cc_start: 0.9241 (mtmt) cc_final: 0.8956 (mtmm) REVERT: R 73 ASP cc_start: 0.8125 (t0) cc_final: 0.7387 (t0) REVERT: S 79 LYS cc_start: 0.6378 (mmmt) cc_final: 0.6038 (tttm) REVERT: S 80 ILE cc_start: 0.7103 (mt) cc_final: 0.6715 (mm) outliers start: 94 outliers final: 72 residues processed: 665 average time/residue: 0.3684 time to fit residues: 374.1807 Evaluate side-chains 669 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 593 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 77 GLU 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 257 HIS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 89 LEU 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 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 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 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 36 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 164 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 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 142 VAL 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 P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 156 VAL 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 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 164 THR Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 192 VAL 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 201 VAL 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 47 CYS Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 104 LEU 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 R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 119 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 165 optimal weight: 0.2980 chunk 277 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN D 202 GLN E 227 ASN G 152 GLN K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN J 152 GLN N 67 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106924 restraints weight = 37149.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110673 restraints weight = 21185.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113108 restraints weight = 14902.044| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 23234 Z= 0.378 Angle : 0.670 11.328 31746 Z= 0.340 Chirality : 0.047 0.239 3580 Planarity : 0.005 0.054 4038 Dihedral : 4.980 26.317 3096 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.30 % Allowed : 21.14 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2826 helix: -2.03 (0.51), residues: 102 sheet: -0.63 (0.18), residues: 792 loop : -1.12 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 104 HIS 0.005 0.001 HIS I 109 PHE 0.026 0.002 PHE O 27 TYR 0.023 0.002 TYR F 106 ARG 0.007 0.001 ARG D 120 *********************** 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 699 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 592 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 MET cc_start: 0.7693 (ttp) cc_final: 0.7399 (tmm) REVERT: D 230 MET cc_start: 0.7494 (ptp) cc_final: 0.7215 (ptp) REVERT: E 118 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8157 (tp-100) REVERT: E 147 VAL cc_start: 0.8577 (t) cc_final: 0.8119 (p) REVERT: E 183 MET cc_start: 0.8818 (ttm) cc_final: 0.8215 (ttm) REVERT: E 206 ASP cc_start: 0.8715 (t70) cc_final: 0.8366 (t0) REVERT: E 222 TYR cc_start: 0.6629 (m-80) cc_final: 0.6154 (m-80) REVERT: G 199 ASN cc_start: 0.9070 (t0) cc_final: 0.8538 (t0) REVERT: G 231 GLU cc_start: 0.8580 (pt0) cc_final: 0.8174 (pt0) REVERT: I 102 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7277 (p90) REVERT: I 155 GLN cc_start: 0.9117 (tp40) cc_final: 0.8504 (tm-30) REVERT: I 241 MET cc_start: 0.7693 (mmm) cc_final: 0.7303 (mtp) REVERT: K 231 ASP cc_start: 0.8924 (t0) cc_final: 0.8503 (t0) REVERT: M 14 LEU cc_start: 0.8985 (mt) cc_final: 0.8653 (tt) REVERT: M 48 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8084 (mtt-85) REVERT: M 50 GLU cc_start: 0.8272 (pm20) cc_final: 0.7870 (pm20) REVERT: O 19 LYS cc_start: 0.8505 (ptmt) cc_final: 0.8182 (ptmt) REVERT: O 59 MET cc_start: 0.7167 (ttp) cc_final: 0.6515 (ttp) REVERT: O 63 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8967 (mtmm) REVERT: P 24 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7663 (ttpp) REVERT: P 80 ILE cc_start: 0.7236 (mt) cc_final: 0.6890 (mm) REVERT: F 95 MET cc_start: 0.7611 (mmm) cc_final: 0.7134 (tpt) REVERT: F 154 MET cc_start: 0.6356 (ttt) cc_final: 0.6120 (mtp) REVERT: H 110 ASP cc_start: 0.9062 (t0) cc_final: 0.8820 (t0) REVERT: H 183 MET cc_start: 0.8761 (ttm) cc_final: 0.8252 (ttm) REVERT: H 206 ASP cc_start: 0.8797 (t70) cc_final: 0.8438 (t0) REVERT: J 30 ASN cc_start: 0.8201 (m-40) cc_final: 0.7925 (t0) REVERT: J 199 ASN cc_start: 0.9069 (t0) cc_final: 0.8553 (t0) REVERT: J 231 GLU cc_start: 0.8532 (pt0) cc_final: 0.8183 (pt0) REVERT: L 102 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7163 (p90) REVERT: L 241 MET cc_start: 0.7715 (mmm) cc_final: 0.7350 (mtp) REVERT: N 231 ASP cc_start: 0.8772 (t0) cc_final: 0.8510 (t0) REVERT: Q 14 LEU cc_start: 0.9035 (mt) cc_final: 0.8732 (tt) REVERT: Q 48 ARG cc_start: 0.8620 (mtt90) cc_final: 0.8297 (ttm-80) REVERT: Q 50 GLU cc_start: 0.8272 (pm20) cc_final: 0.7872 (pm20) REVERT: R 19 LYS cc_start: 0.8460 (ptmt) cc_final: 0.8146 (ptmm) REVERT: R 22 CYS cc_start: 0.8920 (p) cc_final: 0.8570 (p) REVERT: R 23 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8578 (mmmm) REVERT: R 63 LYS cc_start: 0.9253 (mtmt) cc_final: 0.8923 (mtmm) REVERT: S 79 LYS cc_start: 0.6399 (mmmt) cc_final: 0.6113 (tttm) REVERT: S 80 ILE cc_start: 0.7276 (mt) cc_final: 0.6857 (mm) REVERT: S 112 LYS cc_start: 0.5700 (tptt) cc_final: 0.5498 (tptt) outliers start: 107 outliers final: 84 residues processed: 662 average time/residue: 0.3563 time to fit residues: 360.9591 Evaluate side-chains 670 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 584 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 77 GLU 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 248 THR Chi-restraints excluded: chain D residue 257 HIS 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 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 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 127 LEU 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 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 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 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 142 VAL 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 P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 247 ILE 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 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 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 190 CYS Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 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 156 VAL Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 105 CYS 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 R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 21 ILE 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 31 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 247 optimal weight: 0.0370 chunk 202 optimal weight: 0.0870 chunk 237 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN E 227 ASN G 152 GLN K 29 HIS K 97 GLN ** K 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 199 GLN P 6 GLN P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN H 227 ASN J 152 GLN L 155 GLN N 97 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115414 restraints weight = 36826.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119289 restraints weight = 21041.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121839 restraints weight = 14755.220| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23234 Z= 0.160 Angle : 0.598 10.985 31746 Z= 0.301 Chirality : 0.044 0.217 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.525 24.315 3096 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.77 % Allowed : 22.91 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 2826 helix: -2.08 (0.49), residues: 104 sheet: -0.50 (0.18), residues: 762 loop : -0.89 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 203 HIS 0.004 0.001 HIS L 145 PHE 0.028 0.001 PHE N 28 TYR 0.027 0.001 TYR M 135 ARG 0.007 0.001 ARG O 87 ********************** 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 686 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 617 time to evaluate : 2.732 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: 0.7594 (ttp) cc_final: 0.7320 (tmm) REVERT: D 203 TRP cc_start: 0.8561 (m100) cc_final: 0.8317 (m100) REVERT: E 146 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7655 (mt) REVERT: E 147 VAL cc_start: 0.8532 (t) cc_final: 0.7984 (p) REVERT: E 176 ASN cc_start: 0.8882 (m-40) cc_final: 0.8314 (p0) REVERT: E 183 MET cc_start: 0.8830 (ttm) cc_final: 0.8488 (ttm) REVERT: E 206 ASP cc_start: 0.8645 (t70) cc_final: 0.8221 (t0) REVERT: E 222 TYR cc_start: 0.6555 (m-80) cc_final: 0.5994 (m-80) REVERT: E 276 ASN cc_start: 0.8722 (p0) cc_final: 0.8394 (p0) REVERT: E 278 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8323 (m-40) REVERT: G 64 PHE cc_start: 0.9186 (m-80) cc_final: 0.8840 (m-80) REVERT: G 103 ARG cc_start: 0.8597 (ptm160) cc_final: 0.8281 (ptm160) REVERT: G 199 ASN cc_start: 0.9038 (t0) cc_final: 0.8555 (t0) REVERT: G 231 GLU cc_start: 0.8595 (pt0) cc_final: 0.8061 (pt0) REVERT: I 100 TYR cc_start: 0.6368 (t80) cc_final: 0.6045 (t80) REVERT: I 155 GLN cc_start: 0.9019 (tp40) cc_final: 0.8523 (tm-30) REVERT: I 241 MET cc_start: 0.7668 (mmm) cc_final: 0.7327 (mtp) REVERT: K 92 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.8088 (mtp85) REVERT: K 231 ASP cc_start: 0.8873 (t0) cc_final: 0.8467 (t0) REVERT: M 14 LEU cc_start: 0.8994 (mt) cc_final: 0.8598 (tt) REVERT: M 136 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8917 (p) REVERT: O 19 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7934 (ptmm) REVERT: O 59 MET cc_start: 0.7096 (ttp) cc_final: 0.6612 (ttp) REVERT: O 73 ASP cc_start: 0.8144 (t0) cc_final: 0.7363 (t0) REVERT: P 80 ILE cc_start: 0.6753 (mt) cc_final: 0.6418 (mm) REVERT: F 95 MET cc_start: 0.7511 (mmm) cc_final: 0.7059 (tpt) REVERT: H 110 ASP cc_start: 0.8960 (t0) cc_final: 0.8707 (t0) REVERT: H 183 MET cc_start: 0.8724 (ttm) cc_final: 0.8140 (ttm) REVERT: J 30 ASN cc_start: 0.8038 (m-40) cc_final: 0.7813 (t0) REVERT: J 81 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8421 (mttp) REVERT: J 197 TYR cc_start: 0.8611 (t80) cc_final: 0.8341 (t80) REVERT: J 199 ASN cc_start: 0.9022 (t0) cc_final: 0.8384 (t0) REVERT: J 231 GLU cc_start: 0.8555 (pt0) cc_final: 0.8250 (pt0) REVERT: L 100 TYR cc_start: 0.6225 (t80) cc_final: 0.5848 (t80) REVERT: L 241 MET cc_start: 0.7690 (mmm) cc_final: 0.7367 (mtp) REVERT: N 92 ARG cc_start: 0.8737 (ptp-110) cc_final: 0.8064 (mtp85) REVERT: R 19 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7909 (ptmm) REVERT: R 22 CYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8544 (p) REVERT: R 59 MET cc_start: 0.7507 (ttp) cc_final: 0.7286 (ttp) REVERT: R 63 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8854 (mtmm) REVERT: R 73 ASP cc_start: 0.8174 (t0) cc_final: 0.7412 (t0) REVERT: S 79 LYS cc_start: 0.6243 (mmmt) cc_final: 0.5901 (tttm) REVERT: S 80 ILE cc_start: 0.6847 (mt) cc_final: 0.6425 (mm) REVERT: S 112 LYS cc_start: 0.5668 (tptt) cc_final: 0.5442 (tptt) outliers start: 69 outliers final: 50 residues processed: 656 average time/residue: 0.3651 time to fit residues: 366.5177 Evaluate side-chains 649 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 595 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 89 LEU 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 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 173 SER 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 I residue 231 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain M residue 70 CYS 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 O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 255 ILE 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 164 THR Chi-restraints excluded: chain H residue 182 LYS 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 115 SER Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain N residue 47 CYS 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 142 VAL Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain S residue 21 ILE 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 1 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 197 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 227 ASN G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN H 227 ASN J 152 GLN ** N 97 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 = 0.3666 r_free = 0.3666 target = 0.141249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112635 restraints weight = 36679.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116378 restraints weight = 21158.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118831 restraints weight = 14922.209| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23234 Z= 0.186 Angle : 0.596 9.906 31746 Z= 0.298 Chirality : 0.044 0.210 3580 Planarity : 0.004 0.048 4038 Dihedral : 4.455 24.688 3096 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.77 % Allowed : 22.91 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2826 helix: -1.98 (0.47), residues: 116 sheet: -0.55 (0.18), residues: 798 loop : -0.82 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 203 HIS 0.003 0.001 HIS L 145 PHE 0.027 0.001 PHE R 27 TYR 0.024 0.002 TYR P 92 ARG 0.007 0.000 ARG R 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8397.99 seconds wall clock time: 151 minutes 39.94 seconds (9099.94 seconds total)