Starting phenix.real_space_refine on Thu Jun 19 07:34:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9b_38171/06_2025/8x9b_38171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9b_38171/06_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_38171/06_2025/8x9b_38171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9b_38171/06_2025/8x9b_38171.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9b_38171/06_2025/8x9b_38171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9b_38171/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.61, per 1000 atoms: 0.65 Number of scatterers: 22600 At special positions: 0 Unit cell: (193.76, 148.96, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4136 8.00 N 3762 7.00 C 14562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 93 " distance=2.06 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 93 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 3.1 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: 3.87 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: 8.06 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3630 1.31 - 1.44: 6544 1.44 - 1.56: 12846 1.56 - 1.69: 2 1.69 - 1.81: 212 Bond restraints: 23234 Sorted by residual: bond pdb=" N PRO G 163 " pdb=" CD PRO G 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.88e+01 bond pdb=" N PRO J 163 " pdb=" CD PRO J 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.79e+01 bond pdb=" CA LEU L 172 " pdb=" C LEU L 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA LEU I 172 " pdb=" C LEU I 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.19e-02 7.06e+03 3.67e+01 ... (remaining 23229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 30296 3.31 - 6.62: 1257 6.62 - 9.93: 141 9.93 - 13.24: 34 13.24 - 16.55: 18 Bond angle restraints: 31746 Sorted by residual: angle pdb=" N ALA O 101 " pdb=" CA ALA O 101 " pdb=" C ALA O 101 " ideal model delta sigma weight residual 111.36 127.05 -15.69 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N ALA R 101 " pdb=" CA ALA R 101 " pdb=" C ALA R 101 " ideal model delta sigma weight residual 111.36 127.03 -15.67 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N HIS L 145 " pdb=" CA HIS L 145 " pdb=" C HIS L 145 " ideal model delta sigma weight residual 108.13 95.41 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" N HIS I 145 " pdb=" CA HIS I 145 " pdb=" C HIS I 145 " ideal model delta sigma weight residual 108.13 95.42 12.71 9.00e-01 1.23e+00 1.99e+02 angle pdb=" N PHE G 82 " pdb=" CA PHE G 82 " pdb=" C PHE G 82 " ideal model delta sigma weight residual 112.35 128.90 -16.55 1.34e+00 5.57e-01 1.52e+02 ... (remaining 31741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 12666 17.30 - 34.60: 812 34.60 - 51.90: 120 51.90 - 69.20: 38 69.20 - 86.50: 20 Dihedral angle restraints: 13656 sinusoidal: 5286 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS S 23 " pdb=" SG CYS S 23 " pdb=" SG CYS S 93 " pdb=" CB CYS S 93 " ideal model delta sinusoidal sigma weight residual 93.00 150.82 -57.82 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 93 " pdb=" CB CYS P 93 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CA PHE G 82 " pdb=" CB PHE G 82 " ideal model delta harmonic sigma weight residual 122.80 133.63 -10.83 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 13653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3054 0.136 - 0.272: 477 0.272 - 0.409: 41 0.409 - 0.545: 6 0.545 - 0.681: 2 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CA PHE G 82 " pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CB PHE G 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE J 82 " pdb=" N PHE J 82 " pdb=" C PHE J 82 " pdb=" CB PHE J 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TRP F 261 " pdb=" N TRP F 261 " pdb=" C TRP F 261 " pdb=" CB TRP F 261 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 3577 not shown) Planarity restraints: 4038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR P 36 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR P 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR P 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR P 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR S 36 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR S 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR S 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR S 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 186 " 0.331 9.50e-02 1.11e+02 1.48e-01 1.36e+01 pdb=" NE ARG I 186 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG I 186 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG I 186 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 186 " 0.010 2.00e-02 2.50e+03 ... (remaining 4035 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1908 2.72 - 3.26: 20342 3.26 - 3.81: 33898 3.81 - 4.35: 39941 4.35 - 4.90: 71342 Nonbonded interactions: 167431 Sorted by model distance: nonbonded pdb=" N ALA I 168 " pdb=" O ALA I 168 " model vdw 2.173 2.496 nonbonded pdb=" N ALA L 168 " pdb=" O ALA L 168 " model vdw 2.174 2.496 nonbonded pdb=" N TRP O 104 " pdb=" O TRP O 104 " model vdw 2.267 2.496 nonbonded pdb=" N TRP R 104 " pdb=" O TRP R 104 " model vdw 2.267 2.496 nonbonded pdb=" N TYR D 116 " pdb=" O TYR D 116 " model vdw 2.289 2.496 ... (remaining 167426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 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: 0.620 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: 0.040 Extract box with map and model: 0.850 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 54.900 Find NCS groups from input model: 0.430 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.139 23238 Z= 0.836 Angle : 1.573 16.548 31754 Z= 1.020 Chirality : 0.100 0.681 3580 Planarity : 0.011 0.148 4038 Dihedral : 12.253 86.504 8260 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.29513 ( 534) hydrogen bonds : angle 8.80918 ( 1536) SS BOND : bond 0.02169 ( 4) SS BOND : angle 3.62614 ( 8) covalent geometry : bond 0.01196 (23234) covalent geometry : angle 1.57240 (31746) *********************** 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 : 2.638 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: 0.3688 time to fit residues: 560.0971 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 : 2.278 ------------------------------------------------------------------------------- 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: 5.9990 chunk 165 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 208 ASN 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: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114999 restraints weight = 36871.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118734 restraints weight = 20860.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121181 restraints weight = 14572.181| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 23238 Z= 0.206 Angle : 0.685 10.171 31754 Z= 0.356 Chirality : 0.048 0.205 3580 Planarity : 0.006 0.063 4038 Dihedral : 5.160 27.664 3096 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.58 % Allowed : 13.79 % Favored : 82.64 % 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: -2.36 (0.14), residues: 2826 helix: -3.33 (0.33), residues: 122 sheet: -1.22 (0.17), residues: 814 loop : -1.66 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 171 HIS 0.006 0.001 HIS L 145 PHE 0.025 0.002 PHE R 27 TYR 0.027 0.002 TYR P 92 ARG 0.009 0.001 ARG M 68 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 534) hydrogen bonds : angle 6.08406 ( 1536) SS BOND : bond 0.01346 ( 4) SS BOND : angle 1.63269 ( 8) covalent geometry : bond 0.00474 (23234) covalent geometry : angle 0.68437 (31746) *********************** 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 804 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 715 time to evaluate : 2.563 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: 0.8888 (tp40) cc_final: 0.8569 (tp-100) REVERT: D 143 ASN cc_start: 0.8844 (p0) cc_final: 0.8533 (p0) REVERT: D 205 TYR cc_start: 0.8194 (t80) cc_final: 0.7867 (t80) REVERT: D 278 ASN cc_start: 0.8608 (m110) cc_final: 0.8375 (m110) REVERT: D 279 TYR cc_start: 0.8716 (p90) cc_final: 0.8214 (p90) REVERT: D 286 CYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7038 (t) REVERT: E 119 LEU cc_start: 0.8643 (tp) cc_final: 0.8418 (tp) REVERT: E 147 VAL cc_start: 0.8431 (t) cc_final: 0.7876 (p) REVERT: E 149 GLN cc_start: 0.8296 (tp-100) cc_final: 0.8063 (tp40) REVERT: E 150 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8622 (mm) REVERT: E 183 MET cc_start: 0.8953 (ttm) cc_final: 0.8399 (ttm) REVERT: G 30 ASN cc_start: 0.8037 (m-40) cc_final: 0.7765 (t0) REVERT: G 62 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7093 (mmm160) REVERT: G 74 ASP cc_start: 0.7405 (p0) cc_final: 0.7180 (p0) REVERT: G 104 SER cc_start: 0.9032 (t) cc_final: 0.8806 (m) REVERT: G 130 TYR cc_start: 0.8864 (t80) cc_final: 0.8590 (t80) REVERT: G 155 GLN cc_start: 0.7319 (mp10) cc_final: 0.7108 (mp10) REVERT: G 164 TYR cc_start: 0.9186 (t80) cc_final: 0.8861 (t80) REVERT: G 199 ASN cc_start: 0.8959 (t0) cc_final: 0.8638 (t0) REVERT: G 231 GLU cc_start: 0.8544 (pt0) cc_final: 0.8278 (pt0) REVERT: I 30 ASN cc_start: 0.7415 (m-40) cc_final: 0.6968 (p0) REVERT: I 76 LYS cc_start: 0.8966 (mttt) cc_final: 0.8628 (mtpp) REVERT: I 84 ASP cc_start: 0.8128 (t70) cc_final: 0.7879 (t0) REVERT: I 209 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8418 (t70) REVERT: I 223 ASP cc_start: 0.8683 (t0) cc_final: 0.8420 (m-30) REVERT: K 28 PHE cc_start: 0.8111 (t80) cc_final: 0.7799 (t80) REVERT: K 78 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8488 (mmmt) REVERT: K 226 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7813 (mtt) REVERT: M 74 SER cc_start: 0.8825 (t) cc_final: 0.8590 (p) REVERT: O 3 GLN cc_start: 0.7793 (pt0) cc_final: 0.7441 (pm20) REVERT: O 19 LYS cc_start: 0.8181 (ptmt) cc_final: 0.7840 (ptmm) REVERT: P 3 VAL cc_start: 0.8649 (t) cc_final: 0.8275 (p) REVERT: P 4 MET cc_start: 0.8949 (mmm) cc_final: 0.8532 (mmm) REVERT: P 54 TYR cc_start: 0.7285 (t80) cc_final: 0.7081 (t80) REVERT: P 97 THR cc_start: 0.8727 (m) cc_final: 0.8398 (p) REVERT: F 76 GLN cc_start: 0.8841 (tp40) cc_final: 0.8479 (tp-100) REVERT: F 143 ASN cc_start: 0.8765 (p0) cc_final: 0.8444 (p0) REVERT: F 278 ASN cc_start: 0.8602 (m110) cc_final: 0.8380 (m110) REVERT: F 279 TYR cc_start: 0.8860 (p90) cc_final: 0.8599 (p90) REVERT: H 147 VAL cc_start: 0.8414 (t) cc_final: 0.7984 (p) REVERT: H 154 MET cc_start: 0.8324 (ttp) cc_final: 0.8123 (ttm) REVERT: H 183 MET cc_start: 0.8900 (ttm) cc_final: 0.8309 (ttm) REVERT: J 127 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8229 (tp) REVERT: J 164 TYR cc_start: 0.9185 (t80) cc_final: 0.8935 (t80) REVERT: J 199 ASN cc_start: 0.9011 (t0) cc_final: 0.8670 (t0) REVERT: J 231 GLU cc_start: 0.8492 (pt0) cc_final: 0.8234 (pt0) REVERT: L 30 ASN cc_start: 0.7448 (m-40) cc_final: 0.7058 (p0) REVERT: L 76 LYS cc_start: 0.8915 (mttt) cc_final: 0.8550 (mtpp) REVERT: L 84 ASP cc_start: 0.8168 (t70) cc_final: 0.7841 (t0) REVERT: N 78 LYS cc_start: 0.8734 (mptt) cc_final: 0.8521 (mmmt) REVERT: Q 59 LYS cc_start: 0.8907 (tptp) cc_final: 0.8522 (tptp) REVERT: Q 74 SER cc_start: 0.8722 (t) cc_final: 0.8520 (p) REVERT: Q 78 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7537 (tmtt) REVERT: R 3 GLN cc_start: 0.7821 (pt0) cc_final: 0.7518 (pm20) REVERT: R 19 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7805 (ptmm) REVERT: R 98 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7627 (ptm-80) REVERT: S 38 VAL cc_start: 0.8479 (t) cc_final: 0.8279 (m) REVERT: S 80 ILE cc_start: 0.7254 (mt) cc_final: 0.7000 (mm) REVERT: S 95 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7649 (tm-30) outliers start: 89 outliers final: 60 residues processed: 756 average time/residue: 0.3838 time to fit residues: 451.8478 Evaluate side-chains 708 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 641 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 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 190 CYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain 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 111 ILE 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 75 SER 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 164 SER Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 98 ARG 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: 4.9990 chunk 237 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 0.0670 chunk 180 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 245 HIS E 227 ASN E 276 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 ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN F 278 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111835 restraints weight = 37116.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115666 restraints weight = 20978.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118184 restraints weight = 14574.197| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23238 Z= 0.117 Angle : 0.590 8.587 31754 Z= 0.299 Chirality : 0.045 0.230 3580 Planarity : 0.005 0.054 4038 Dihedral : 4.757 26.087 3096 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.30 % Allowed : 16.00 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.88 (0.14), residues: 2826 helix: -3.10 (0.37), residues: 122 sheet: -0.89 (0.17), residues: 836 loop : -1.32 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 171 HIS 0.007 0.001 HIS I 209 PHE 0.020 0.001 PHE R 27 TYR 0.020 0.001 TYR F 106 ARG 0.005 0.001 ARG M 68 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 534) hydrogen bonds : angle 5.52425 ( 1536) SS BOND : bond 0.00424 ( 4) SS BOND : angle 1.11204 ( 8) covalent geometry : bond 0.00272 (23234) covalent geometry : angle 0.58980 (31746) *********************** 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 779 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 672 time to evaluate : 2.428 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: 0.8647 (tp40) cc_final: 0.7953 (tm-30) REVERT: D 82 ASN cc_start: 0.8759 (m110) cc_final: 0.7971 (m-40) REVERT: D 143 ASN cc_start: 0.8844 (p0) cc_final: 0.8587 (p0) REVERT: D 185 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7846 (t0) REVERT: E 150 LEU cc_start: 0.9191 (tp) cc_final: 0.8627 (mm) REVERT: E 162 LYS cc_start: 0.8774 (mttm) cc_final: 0.8496 (mtpp) REVERT: E 183 MET cc_start: 0.8985 (ttm) cc_final: 0.8782 (ttm) REVERT: G 74 ASP cc_start: 0.7471 (p0) cc_final: 0.7269 (p0) REVERT: G 199 ASN cc_start: 0.9044 (t0) cc_final: 0.8588 (t0) REVERT: G 231 GLU cc_start: 0.8461 (pt0) cc_final: 0.8180 (pt0) REVERT: I 76 LYS cc_start: 0.8831 (mttt) cc_final: 0.8575 (mtpp) REVERT: I 84 ASP cc_start: 0.8036 (t70) cc_final: 0.7750 (t0) REVERT: K 78 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8691 (mmmt) REVERT: K 226 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: M 74 SER cc_start: 0.8674 (t) cc_final: 0.8467 (p) REVERT: O 3 GLN cc_start: 0.7717 (pt0) cc_final: 0.7504 (pm20) REVERT: O 19 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7892 (ptmm) REVERT: O 63 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8920 (mtmm) REVERT: P 3 VAL cc_start: 0.8649 (t) cc_final: 0.8253 (p) REVERT: P 4 MET cc_start: 0.9015 (mmm) cc_final: 0.8647 (mmm) REVERT: P 80 ILE cc_start: 0.7102 (mt) cc_final: 0.6857 (mm) REVERT: F 76 GLN cc_start: 0.8806 (tp40) cc_final: 0.8542 (tp40) REVERT: F 185 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7943 (t0) REVERT: H 147 VAL cc_start: 0.8558 (t) cc_final: 0.8142 (p) REVERT: H 149 GLN cc_start: 0.8387 (tp40) cc_final: 0.7961 (tp40) REVERT: H 162 LYS cc_start: 0.8790 (mttm) cc_final: 0.8501 (mtpp) REVERT: H 183 MET cc_start: 0.8964 (ttm) cc_final: 0.8336 (ttm) REVERT: H 275 THR cc_start: 0.8865 (p) cc_final: 0.8559 (t) REVERT: J 30 ASN cc_start: 0.8058 (m-40) cc_final: 0.7841 (t0) REVERT: J 74 ASP cc_start: 0.7460 (p0) cc_final: 0.7223 (p0) REVERT: J 79 TYR cc_start: 0.8884 (p90) cc_final: 0.8620 (p90) REVERT: J 81 LYS cc_start: 0.8742 (mttm) cc_final: 0.8529 (mttm) REVERT: J 199 ASN cc_start: 0.9086 (t0) cc_final: 0.8569 (t0) REVERT: L 76 LYS cc_start: 0.8774 (mttt) cc_final: 0.8523 (mtpp) REVERT: L 84 ASP cc_start: 0.8098 (t70) cc_final: 0.7818 (t0) REVERT: N 14 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9082 (tp) REVERT: Q 59 LYS cc_start: 0.9012 (tptp) cc_final: 0.8674 (tptp) REVERT: R 19 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7871 (ptmm) REVERT: R 63 LYS cc_start: 0.9135 (mtmt) cc_final: 0.8914 (mtmm) REVERT: S 54 TYR cc_start: 0.7023 (t80) cc_final: 0.6469 (t80) REVERT: S 80 ILE cc_start: 0.7107 (mt) cc_final: 0.6865 (mm) REVERT: S 92 TYR cc_start: 0.8863 (m-80) cc_final: 0.8553 (m-80) outliers start: 107 outliers final: 75 residues processed: 728 average time/residue: 0.3430 time to fit residues: 380.4015 Evaluate side-chains 715 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 636 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 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 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 127 LEU 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 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 M residue 204 VAL 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 38 VAL 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 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 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 170 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 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 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 98 ARG Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP 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: 6.9990 chunk 65 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 162 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** E 227 ASN ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN K 29 HIS ** 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 189 GLN F 202 GLN F 245 HIS 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 ** Q 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103650 restraints weight = 37641.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107331 restraints weight = 21285.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109771 restraints weight = 14870.602| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 23238 Z= 0.267 Angle : 0.680 9.137 31754 Z= 0.348 Chirality : 0.048 0.216 3580 Planarity : 0.005 0.054 4038 Dihedral : 5.142 26.948 3096 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.27 % Allowed : 17.12 % Favored : 77.61 % 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: -1.87 (0.14), residues: 2826 helix: -2.95 (0.37), residues: 122 sheet: -0.87 (0.17), residues: 818 loop : -1.33 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 171 HIS 0.005 0.001 HIS I 109 PHE 0.025 0.002 PHE R 27 TYR 0.024 0.002 TYR S 54 ARG 0.011 0.001 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 534) hydrogen bonds : angle 5.55850 ( 1536) SS BOND : bond 0.00819 ( 4) SS BOND : angle 1.65689 ( 8) covalent geometry : bond 0.00631 (23234) covalent geometry : angle 0.67949 (31746) *********************** 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 774 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 643 time to evaluate : 2.413 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: 0.8711 (tp40) cc_final: 0.8226 (tm-30) REVERT: D 82 ASN cc_start: 0.8897 (m110) cc_final: 0.8522 (m-40) REVERT: D 95 MET cc_start: 0.7766 (ttp) cc_final: 0.7451 (tmm) REVERT: E 110 ASP cc_start: 0.8994 (t0) cc_final: 0.8774 (t0) REVERT: E 162 LYS cc_start: 0.8927 (mttm) cc_final: 0.8711 (mtpp) REVERT: G 199 ASN cc_start: 0.9082 (t0) cc_final: 0.8588 (t0) REVERT: I 84 ASP cc_start: 0.8298 (t70) cc_final: 0.8022 (t0) REVERT: K 78 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8754 (mmmt) REVERT: K 226 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7706 (mtp) REVERT: M 48 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8323 (mtt90) REVERT: O 3 GLN cc_start: 0.7886 (pt0) cc_final: 0.7666 (pm20) REVERT: O 19 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8047 (ptmm) REVERT: O 63 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8884 (mtmm) REVERT: P 3 VAL cc_start: 0.8800 (t) cc_final: 0.8569 (t) REVERT: P 80 ILE cc_start: 0.7350 (mt) cc_final: 0.7056 (mm) REVERT: F 76 GLN cc_start: 0.8849 (tp40) cc_final: 0.8481 (tm-30) REVERT: F 82 ASN cc_start: 0.8811 (m110) cc_final: 0.8594 (m-40) REVERT: F 118 GLN cc_start: 0.8203 (mm110) cc_final: 0.7995 (mm110) REVERT: F 195 MET cc_start: 0.7055 (mmm) cc_final: 0.6685 (mmm) REVERT: H 110 ASP cc_start: 0.9017 (t0) cc_final: 0.8794 (t0) REVERT: H 149 GLN cc_start: 0.8543 (tp40) cc_final: 0.8283 (tp-100) REVERT: H 183 MET cc_start: 0.8882 (ttm) cc_final: 0.8493 (ttm) REVERT: H 275 THR cc_start: 0.8860 (p) cc_final: 0.8542 (t) REVERT: J 30 ASN cc_start: 0.8213 (m-40) cc_final: 0.7882 (t0) REVERT: J 199 ASN cc_start: 0.9112 (t0) cc_final: 0.8541 (t0) REVERT: J 231 GLU cc_start: 0.8500 (pt0) cc_final: 0.8296 (pt0) REVERT: L 76 LYS cc_start: 0.8897 (mttt) cc_final: 0.8695 (mtpp) REVERT: L 84 ASP cc_start: 0.8309 (t70) cc_final: 0.8050 (t0) REVERT: L 155 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8601 (tp40) REVERT: N 14 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9172 (tp) REVERT: N 25 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8338 (mt) REVERT: N 231 ASP cc_start: 0.8759 (t70) cc_final: 0.8359 (t0) REVERT: Q 59 LYS cc_start: 0.9147 (tptp) cc_final: 0.8907 (tptp) REVERT: R 19 LYS cc_start: 0.8527 (ptmt) cc_final: 0.7979 (ptmm) REVERT: R 63 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8893 (mtmm) REVERT: S 79 LYS cc_start: 0.6486 (mmmt) cc_final: 0.6164 (tttm) REVERT: S 80 ILE cc_start: 0.7173 (mt) cc_final: 0.6771 (mm) outliers start: 131 outliers final: 108 residues processed: 714 average time/residue: 0.3483 time to fit residues: 383.7374 Evaluate side-chains 713 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 602 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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 295 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain 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 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 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 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 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 55 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 248 THR Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 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 H residue 286 CYS Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 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 127 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain N residue 14 LEU 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 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 55 VAL 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: 7.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 150 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 109 HIS K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 118 GLN H 227 ASN J 152 GLN L 145 HIS L 209 HIS N 67 GLN N 97 GLN ** Q 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109313 restraints weight = 37543.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113023 restraints weight = 21270.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115478 restraints weight = 14815.228| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23238 Z= 0.110 Angle : 0.570 8.009 31754 Z= 0.288 Chirality : 0.044 0.221 3580 Planarity : 0.005 0.050 4038 Dihedral : 4.734 24.878 3096 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.50 % Allowed : 19.05 % Favored : 76.45 % 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: -2.87 (0.37), residues: 122 sheet: -0.71 (0.17), residues: 818 loop : -1.10 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 PHE 0.025 0.001 PHE K 28 TYR 0.025 0.001 TYR F 106 ARG 0.004 0.000 ARG H 236 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 534) hydrogen bonds : angle 5.31733 ( 1536) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.00480 ( 8) covalent geometry : bond 0.00261 (23234) covalent geometry : angle 0.57006 (31746) *********************** 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 744 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 632 time to evaluate : 2.351 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: 0.8702 (tp40) cc_final: 0.8371 (tm-30) REVERT: D 82 ASN cc_start: 0.8861 (m110) cc_final: 0.8602 (m-40) REVERT: E 110 ASP cc_start: 0.8932 (t0) cc_final: 0.8713 (t0) REVERT: E 162 LYS cc_start: 0.8880 (mttm) cc_final: 0.8671 (mtpp) REVERT: E 183 MET cc_start: 0.8888 (ttm) cc_final: 0.8434 (ttm) REVERT: E 206 ASP cc_start: 0.8579 (t70) cc_final: 0.8166 (t0) REVERT: G 199 ASN cc_start: 0.9096 (t0) cc_final: 0.8639 (t0) REVERT: I 84 ASP cc_start: 0.8158 (t70) cc_final: 0.7931 (t0) REVERT: I 241 MET cc_start: 0.7956 (mmm) cc_final: 0.7430 (mtp) REVERT: K 226 MET cc_start: 0.7950 (mtt) cc_final: 0.7668 (mtt) REVERT: O 19 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7873 (ptmm) REVERT: O 59 MET cc_start: 0.6994 (ttp) cc_final: 0.6764 (ttp) REVERT: O 63 LYS cc_start: 0.9268 (mtmt) cc_final: 0.8924 (mtmm) REVERT: O 95 TYR cc_start: 0.8808 (m-80) cc_final: 0.8582 (m-80) REVERT: P 3 VAL cc_start: 0.8632 (t) cc_final: 0.8360 (t) REVERT: P 4 MET cc_start: 0.9042 (mmm) cc_final: 0.8726 (mmm) REVERT: P 80 ILE cc_start: 0.7212 (mt) cc_final: 0.6890 (mm) REVERT: F 76 GLN cc_start: 0.8765 (tp40) cc_final: 0.8371 (tm-30) REVERT: F 82 ASN cc_start: 0.8759 (m110) cc_final: 0.8512 (m-40) REVERT: H 110 ASP cc_start: 0.8947 (t0) cc_final: 0.8735 (t0) REVERT: H 118 GLN cc_start: 0.8551 (tp40) cc_final: 0.8343 (tp-100) REVERT: J 30 ASN cc_start: 0.8185 (m-40) cc_final: 0.7863 (t0) REVERT: J 197 TYR cc_start: 0.8631 (t80) cc_final: 0.8348 (t80) REVERT: J 199 ASN cc_start: 0.9077 (t0) cc_final: 0.8322 (t0) REVERT: J 231 GLU cc_start: 0.8518 (pt0) cc_final: 0.8274 (pt0) REVERT: L 76 LYS cc_start: 0.8737 (mttt) cc_final: 0.8502 (mtpp) REVERT: L 84 ASP cc_start: 0.8144 (t70) cc_final: 0.7939 (t0) REVERT: L 241 MET cc_start: 0.8009 (mmm) cc_final: 0.7459 (mtp) REVERT: N 14 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9092 (tp) REVERT: N 231 ASP cc_start: 0.8694 (t70) cc_final: 0.8314 (t0) REVERT: Q 48 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8089 (mtt-85) REVERT: Q 59 LYS cc_start: 0.9197 (tptp) cc_final: 0.8909 (tptp) REVERT: R 19 LYS cc_start: 0.8300 (ptmt) cc_final: 0.7960 (ptmm) REVERT: R 63 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8958 (mtmm) REVERT: R 95 TYR cc_start: 0.8793 (m-80) cc_final: 0.8568 (m-80) REVERT: S 79 LYS cc_start: 0.6464 (mmmt) cc_final: 0.6187 (tttm) REVERT: S 80 ILE cc_start: 0.7020 (mt) cc_final: 0.6623 (mm) REVERT: S 92 TYR cc_start: 0.8987 (m-80) cc_final: 0.8555 (m-80) outliers start: 112 outliers final: 77 residues processed: 706 average time/residue: 0.3391 time to fit residues: 366.1970 Evaluate side-chains 692 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 614 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 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 127 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 55 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 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 78 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN 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 143 ASN 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 H residue 286 CYS 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 L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 145 HIS 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 164 SER Chi-restraints excluded: chain N residue 225 THR 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 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 55 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 98 ARG Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 143 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 227 ASN J 152 GLN L 145 HIS L 155 GLN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.135561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106962 restraints weight = 37481.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110648 restraints weight = 21437.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113076 restraints weight = 14988.755| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23238 Z= 0.152 Angle : 0.577 10.551 31754 Z= 0.292 Chirality : 0.045 0.210 3580 Planarity : 0.005 0.050 4038 Dihedral : 4.673 24.986 3096 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.78 % Allowed : 19.29 % Favored : 75.92 % 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: -1.53 (0.15), residues: 2826 helix: -2.56 (0.40), residues: 122 sheet: -0.69 (0.17), residues: 816 loop : -1.08 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 171 HIS 0.017 0.001 HIS L 145 PHE 0.026 0.001 PHE K 28 TYR 0.025 0.002 TYR F 106 ARG 0.007 0.000 ARG O 87 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 534) hydrogen bonds : angle 5.25601 ( 1536) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.83811 ( 8) covalent geometry : bond 0.00367 (23234) covalent geometry : angle 0.57708 (31746) *********************** 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 728 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 609 time to evaluate : 2.491 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: 0.8761 (tp40) cc_final: 0.8378 (tm-30) REVERT: D 82 ASN cc_start: 0.8852 (m110) cc_final: 0.8575 (m-40) REVERT: E 110 ASP cc_start: 0.9078 (t0) cc_final: 0.8861 (t0) REVERT: E 162 LYS cc_start: 0.8948 (mttm) cc_final: 0.8671 (mtpp) REVERT: E 183 MET cc_start: 0.8898 (ttm) cc_final: 0.8234 (ttm) REVERT: E 206 ASP cc_start: 0.8705 (t70) cc_final: 0.8272 (t0) REVERT: E 278 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8618 (m-40) REVERT: G 199 ASN cc_start: 0.9045 (t0) cc_final: 0.8529 (t0) REVERT: I 84 ASP cc_start: 0.8305 (t70) cc_final: 0.8002 (t0) REVERT: I 102 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6811 (p90) REVERT: I 241 MET cc_start: 0.7910 (mmm) cc_final: 0.7338 (mtp) REVERT: K 226 MET cc_start: 0.8151 (mtt) cc_final: 0.7825 (mtp) REVERT: O 19 LYS cc_start: 0.8354 (ptmt) cc_final: 0.7993 (ptmm) REVERT: O 63 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8874 (mtmm) REVERT: O 95 TYR cc_start: 0.8827 (m-80) cc_final: 0.8568 (m-80) REVERT: P 3 VAL cc_start: 0.8882 (t) cc_final: 0.8678 (t) REVERT: P 80 ILE cc_start: 0.7150 (mt) cc_final: 0.6752 (mm) REVERT: F 76 GLN cc_start: 0.8789 (tp40) cc_final: 0.8394 (tm-30) REVERT: F 82 ASN cc_start: 0.8742 (m110) cc_final: 0.8508 (m-40) REVERT: H 110 ASP cc_start: 0.9120 (t0) cc_final: 0.8893 (t0) REVERT: H 149 GLN cc_start: 0.8569 (tp40) cc_final: 0.8226 (tp40) REVERT: H 183 MET cc_start: 0.8869 (ttm) cc_final: 0.8326 (ttm) REVERT: J 30 ASN cc_start: 0.8288 (m-40) cc_final: 0.7904 (t0) REVERT: J 197 TYR cc_start: 0.8695 (t80) cc_final: 0.8294 (t80) REVERT: J 199 ASN cc_start: 0.9034 (t0) cc_final: 0.8225 (t0) REVERT: J 231 GLU cc_start: 0.8570 (pt0) cc_final: 0.8295 (pt0) REVERT: L 76 LYS cc_start: 0.8805 (mttt) cc_final: 0.8542 (mtpp) REVERT: L 84 ASP cc_start: 0.8267 (t70) cc_final: 0.8025 (t0) REVERT: L 102 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.6945 (p90) REVERT: L 241 MET cc_start: 0.7919 (mmm) cc_final: 0.7385 (mtp) REVERT: Q 48 ARG cc_start: 0.8618 (mtt90) cc_final: 0.8147 (mmt90) REVERT: Q 59 LYS cc_start: 0.9325 (tptp) cc_final: 0.8987 (tptp) REVERT: R 19 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7924 (ptmm) REVERT: R 63 LYS cc_start: 0.9224 (mtmt) cc_final: 0.8897 (mtmm) REVERT: S 24 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7663 (ttpp) REVERT: S 54 TYR cc_start: 0.6982 (t80) cc_final: 0.6628 (t80) REVERT: S 79 LYS cc_start: 0.6418 (mmmt) cc_final: 0.6174 (tttm) REVERT: S 80 ILE cc_start: 0.7134 (mt) cc_final: 0.6705 (mm) REVERT: S 92 TYR cc_start: 0.8957 (m-80) cc_final: 0.8492 (m-80) outliers start: 119 outliers final: 89 residues processed: 686 average time/residue: 0.3538 time to fit residues: 374.9810 Evaluate side-chains 684 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 592 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 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 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN 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 127 LEU 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 201 VAL Chi-restraints excluded: chain G residue 235 THR 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 127 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain M residue 55 VAL 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 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 55 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 O residue 103 TYR Chi-restraints excluded: chain P residue 42 GLN 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 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS 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 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 50 GLU Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 55 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 98 ARG Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 103 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 251 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 161 optimal weight: 0.0670 chunk 268 optimal weight: 0.1980 chunk 185 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 225 ASN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 227 ASN J 152 GLN J 225 ASN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN S 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113055 restraints weight = 36847.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116992 restraints weight = 20598.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119560 restraints weight = 14259.566| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23238 Z= 0.095 Angle : 0.557 13.010 31754 Z= 0.280 Chirality : 0.044 0.175 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.435 23.358 3096 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.90 % Allowed : 20.58 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.43), residues: 122 sheet: -0.54 (0.18), residues: 814 loop : -0.92 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 171 HIS 0.003 0.000 HIS L 109 PHE 0.018 0.001 PHE O 27 TYR 0.026 0.001 TYR F 106 ARG 0.007 0.000 ARG O 87 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 534) hydrogen bonds : angle 5.11168 ( 1536) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.63518 ( 8) covalent geometry : bond 0.00222 (23234) covalent geometry : angle 0.55735 (31746) *********************** 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 737 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 640 time to evaluate : 2.923 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: 0.8686 (tp40) cc_final: 0.8389 (tm-30) REVERT: D 82 ASN cc_start: 0.8859 (m110) cc_final: 0.8622 (m-40) REVERT: E 110 ASP cc_start: 0.9009 (t0) cc_final: 0.8779 (t0) REVERT: E 162 LYS cc_start: 0.8929 (mttm) cc_final: 0.8664 (mtpp) REVERT: E 183 MET cc_start: 0.8841 (ttm) cc_final: 0.8321 (ttm) REVERT: E 206 ASP cc_start: 0.8653 (t70) cc_final: 0.8223 (t0) REVERT: E 236 ARG cc_start: 0.7635 (ptt90) cc_final: 0.7125 (ptt90) REVERT: E 278 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8555 (m-40) REVERT: G 199 ASN cc_start: 0.9057 (t0) cc_final: 0.8591 (t0) REVERT: I 84 ASP cc_start: 0.8174 (t70) cc_final: 0.7923 (t0) REVERT: I 102 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6656 (p90) REVERT: I 241 MET cc_start: 0.7786 (mmm) cc_final: 0.7221 (mtp) REVERT: K 226 MET cc_start: 0.8158 (mtt) cc_final: 0.7835 (mtp) REVERT: M 48 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7775 (mtt-85) REVERT: M 224 PHE cc_start: 0.9104 (t80) cc_final: 0.8790 (t80) REVERT: O 19 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7923 (ptmm) REVERT: O 59 MET cc_start: 0.7119 (ttp) cc_final: 0.6787 (ttp) REVERT: O 63 LYS cc_start: 0.9269 (mtmt) cc_final: 0.8909 (mtmm) REVERT: O 98 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7580 (ptm-80) REVERT: P 24 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7749 (ttpp) REVERT: P 80 ILE cc_start: 0.6974 (mt) cc_final: 0.6602 (mm) REVERT: P 112 LYS cc_start: 0.5755 (tptt) cc_final: 0.5359 (tptt) REVERT: F 76 GLN cc_start: 0.8702 (tp40) cc_final: 0.8403 (tm-30) REVERT: F 82 ASN cc_start: 0.8748 (m110) cc_final: 0.8529 (m-40) REVERT: F 253 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7975 (ttp) REVERT: H 106 TYR cc_start: 0.8592 (p90) cc_final: 0.8374 (p90) REVERT: H 110 ASP cc_start: 0.9052 (t0) cc_final: 0.8811 (t0) REVERT: H 173 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8439 (t) REVERT: H 176 ASN cc_start: 0.8841 (m-40) cc_final: 0.8542 (p0) REVERT: H 183 MET cc_start: 0.8846 (ttm) cc_final: 0.8461 (ttm) REVERT: J 30 ASN cc_start: 0.8225 (m-40) cc_final: 0.7807 (t0) REVERT: J 64 PHE cc_start: 0.8899 (m-80) cc_final: 0.8684 (m-80) REVERT: J 197 TYR cc_start: 0.8675 (t80) cc_final: 0.8340 (t80) REVERT: J 199 ASN cc_start: 0.9050 (t0) cc_final: 0.8300 (t0) REVERT: J 231 GLU cc_start: 0.8589 (pt0) cc_final: 0.8290 (pt0) REVERT: L 76 LYS cc_start: 0.8651 (mttt) cc_final: 0.8409 (mtpp) REVERT: L 84 ASP cc_start: 0.8168 (t70) cc_final: 0.7910 (t0) REVERT: Q 48 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8124 (mmt90) REVERT: Q 59 LYS cc_start: 0.9341 (tptp) cc_final: 0.8970 (tptp) REVERT: R 19 LYS cc_start: 0.8218 (ptmt) cc_final: 0.7876 (ptmm) REVERT: R 59 MET cc_start: 0.7149 (ttp) cc_final: 0.6901 (ttp) REVERT: R 63 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8906 (mtmm) REVERT: R 73 ASP cc_start: 0.7980 (t0) cc_final: 0.7074 (t0) REVERT: R 98 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7569 (ptm-80) REVERT: S 4 MET cc_start: 0.9116 (mmm) cc_final: 0.8706 (mmm) REVERT: S 24 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7655 (ttpp) REVERT: S 79 LYS cc_start: 0.6327 (mmmt) cc_final: 0.6099 (tttm) REVERT: S 80 ILE cc_start: 0.7003 (mt) cc_final: 0.6582 (mm) REVERT: S 92 TYR cc_start: 0.8832 (m-80) cc_final: 0.8413 (m-80) outliers start: 97 outliers final: 65 residues processed: 705 average time/residue: 0.4387 time to fit residues: 475.6078 Evaluate side-chains 683 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 612 time to evaluate : 5.512 ------------------------------------------------------------------------------- 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 E residue 89 LEU 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 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 85 VAL 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 201 VAL Chi-restraints excluded: chain I residue 40 GLU 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 231 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 55 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 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 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 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 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 115 SER Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 225 THR 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 164 SER Chi-restraints excluded: chain R residue 55 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 98 ARG Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 263 optimal weight: 0.0050 chunk 198 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 242 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 overall best weight: 2.8600 ------------------------------------------------------------------------------- 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 ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109964 restraints weight = 36989.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113786 restraints weight = 20744.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116281 restraints weight = 14417.851| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23238 Z= 0.164 Angle : 0.591 11.465 31754 Z= 0.297 Chirality : 0.045 0.165 3580 Planarity : 0.004 0.050 4038 Dihedral : 4.560 25.081 3096 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.18 % Allowed : 20.90 % Favored : 74.92 % 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: -1.30 (0.15), residues: 2826 helix: -2.04 (0.48), residues: 112 sheet: -0.59 (0.17), residues: 822 loop : -0.92 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 PHE 0.018 0.001 PHE H 169 TYR 0.026 0.002 TYR D 106 ARG 0.007 0.000 ARG O 87 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 534) hydrogen bonds : angle 5.11051 ( 1536) SS BOND : bond 0.01078 ( 4) SS BOND : angle 1.02428 ( 8) covalent geometry : bond 0.00394 (23234) covalent geometry : angle 0.59101 (31746) *********************** 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 710 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 606 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8688 (tp40) cc_final: 0.8430 (tm-30) REVERT: D 95 MET cc_start: 0.7796 (ttp) cc_final: 0.7444 (tmm) REVERT: E 110 ASP cc_start: 0.8986 (t0) cc_final: 0.8738 (t0) REVERT: E 162 LYS cc_start: 0.8933 (mttm) cc_final: 0.8717 (mtpp) REVERT: E 183 MET cc_start: 0.8781 (ttm) cc_final: 0.8136 (ttm) REVERT: E 206 ASP cc_start: 0.8697 (t70) cc_final: 0.8318 (t0) REVERT: E 278 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8433 (m-40) REVERT: E 280 LYS cc_start: 0.8567 (tttt) cc_final: 0.8127 (tppt) REVERT: G 199 ASN cc_start: 0.9057 (t0) cc_final: 0.8561 (t0) REVERT: G 231 GLU cc_start: 0.8683 (pt0) cc_final: 0.8319 (pt0) REVERT: I 84 ASP cc_start: 0.8185 (t70) cc_final: 0.7962 (t0) REVERT: I 100 TYR cc_start: 0.6285 (t80) cc_final: 0.5972 (t80) REVERT: I 102 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.6906 (p90) REVERT: I 241 MET cc_start: 0.7799 (mmm) cc_final: 0.7259 (mtp) REVERT: K 226 MET cc_start: 0.8105 (mtt) cc_final: 0.7800 (mtp) REVERT: M 14 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8556 (tt) REVERT: M 48 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7884 (mtt-85) REVERT: M 224 PHE cc_start: 0.9055 (t80) cc_final: 0.8689 (t80) REVERT: O 19 LYS cc_start: 0.8421 (ptmt) cc_final: 0.8035 (ptmm) REVERT: O 59 MET cc_start: 0.7132 (ttp) cc_final: 0.6830 (ttp) REVERT: O 63 LYS cc_start: 0.9270 (mtmt) cc_final: 0.8927 (mtmm) REVERT: P 24 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7839 (ttpp) REVERT: P 80 ILE cc_start: 0.7082 (mt) cc_final: 0.6698 (mm) REVERT: P 112 LYS cc_start: 0.5987 (tptt) cc_final: 0.5517 (tptt) REVERT: F 76 GLN cc_start: 0.8753 (tp40) cc_final: 0.8506 (tm-30) REVERT: F 253 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7895 (ttp) REVERT: H 110 ASP cc_start: 0.9032 (t0) cc_final: 0.8805 (t0) REVERT: H 183 MET cc_start: 0.8818 (ttm) cc_final: 0.8292 (ttm) REVERT: H 280 LYS cc_start: 0.8563 (tttt) cc_final: 0.8156 (tppt) REVERT: J 197 TYR cc_start: 0.8709 (t80) cc_final: 0.8394 (t80) REVERT: J 199 ASN cc_start: 0.9064 (t0) cc_final: 0.8335 (t0) REVERT: J 231 GLU cc_start: 0.8504 (pt0) cc_final: 0.8100 (pt0) REVERT: L 102 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.6963 (p90) REVERT: L 241 MET cc_start: 0.7802 (mmm) cc_final: 0.7278 (mtp) REVERT: Q 48 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8156 (mmt90) REVERT: R 19 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8060 (ptmm) REVERT: R 59 MET cc_start: 0.7175 (ttp) cc_final: 0.6900 (ttp) REVERT: R 63 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8920 (mtmm) REVERT: R 73 ASP cc_start: 0.8166 (t0) cc_final: 0.7380 (t0) REVERT: S 24 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7789 (ttpp) REVERT: S 79 LYS cc_start: 0.6341 (mmmt) cc_final: 0.6027 (tttm) REVERT: S 80 ILE cc_start: 0.7114 (mt) cc_final: 0.6718 (mm) REVERT: S 112 LYS cc_start: 0.6128 (tptt) cc_final: 0.5672 (tptt) outliers start: 104 outliers final: 81 residues processed: 672 average time/residue: 0.4224 time to fit residues: 440.5020 Evaluate side-chains 680 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 594 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain E residue 286 CYS 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 127 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain 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 127 LEU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 55 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 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 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 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 N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 67 GLN 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 Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 55 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 119 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 K 97 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN F 82 ASN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 227 ASN H 276 ASN J 152 GLN L 155 GLN N 67 GLN N 97 GLN N 199 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097662 restraints weight = 37836.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101400 restraints weight = 21326.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103879 restraints weight = 14967.176| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23238 Z= 0.155 Angle : 0.597 11.352 31754 Z= 0.300 Chirality : 0.045 0.166 3580 Planarity : 0.004 0.051 4038 Dihedral : 4.609 24.611 3096 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.06 % Allowed : 21.66 % Favored : 74.28 % 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: -1.29 (0.15), residues: 2826 helix: -1.88 (0.51), residues: 102 sheet: -0.59 (0.18), residues: 798 loop : -0.93 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 171 HIS 0.004 0.001 HIS L 109 PHE 0.017 0.001 PHE H 169 TYR 0.027 0.002 TYR D 106 ARG 0.006 0.000 ARG O 87 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 534) hydrogen bonds : angle 5.13452 ( 1536) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.16766 ( 8) covalent geometry : bond 0.00375 (23234) covalent geometry : angle 0.59696 (31746) *********************** 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 700 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 599 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8727 (tp40) cc_final: 0.8459 (tm-30) REVERT: D 95 MET cc_start: 0.7684 (ttp) cc_final: 0.7340 (tmm) REVERT: E 110 ASP cc_start: 0.9111 (t0) cc_final: 0.8811 (t0) REVERT: E 162 LYS cc_start: 0.8990 (mttm) cc_final: 0.8699 (mtpp) REVERT: E 183 MET cc_start: 0.8810 (ttm) cc_final: 0.8094 (ttm) REVERT: E 206 ASP cc_start: 0.8771 (t70) cc_final: 0.8337 (t0) REVERT: E 278 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8523 (m-40) REVERT: G 199 ASN cc_start: 0.9002 (t0) cc_final: 0.8501 (t0) REVERT: G 231 GLU cc_start: 0.8717 (pt0) cc_final: 0.8349 (pt0) REVERT: I 84 ASP cc_start: 0.8249 (t70) cc_final: 0.8005 (t0) REVERT: I 100 TYR cc_start: 0.6413 (t80) cc_final: 0.5966 (t80) REVERT: I 102 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.6799 (p90) REVERT: I 241 MET cc_start: 0.7652 (mmm) cc_final: 0.7186 (mtp) REVERT: K 226 MET cc_start: 0.8231 (mtt) cc_final: 0.7911 (mtp) REVERT: K 231 ASP cc_start: 0.8898 (t0) cc_final: 0.8680 (t0) REVERT: M 14 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8534 (tt) REVERT: M 48 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7827 (mtt-85) REVERT: O 19 LYS cc_start: 0.8323 (ptmt) cc_final: 0.8031 (ptmt) REVERT: O 59 MET cc_start: 0.7246 (ttp) cc_final: 0.6909 (ttp) REVERT: P 24 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7652 (ttpp) REVERT: P 80 ILE cc_start: 0.6955 (mt) cc_final: 0.6546 (mm) REVERT: P 112 LYS cc_start: 0.6155 (tptt) cc_final: 0.5740 (tptt) REVERT: F 76 GLN cc_start: 0.8749 (tp40) cc_final: 0.8532 (tm-30) REVERT: F 253 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: H 110 ASP cc_start: 0.9103 (t0) cc_final: 0.8846 (t0) REVERT: H 149 GLN cc_start: 0.8596 (tp40) cc_final: 0.8109 (tp40) REVERT: H 172 GLN cc_start: 0.8508 (mt0) cc_final: 0.8152 (pp30) REVERT: H 176 ASN cc_start: 0.8898 (m-40) cc_final: 0.8418 (p0) REVERT: H 183 MET cc_start: 0.8858 (ttm) cc_final: 0.8240 (ttm) REVERT: H 206 ASP cc_start: 0.8745 (t70) cc_final: 0.8394 (t0) REVERT: H 280 LYS cc_start: 0.8566 (tttt) cc_final: 0.8039 (tppt) REVERT: J 197 TYR cc_start: 0.8721 (t80) cc_final: 0.8346 (t80) REVERT: J 199 ASN cc_start: 0.9013 (t0) cc_final: 0.8286 (t0) REVERT: J 231 GLU cc_start: 0.8593 (pt0) cc_final: 0.8212 (pt0) REVERT: L 102 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6892 (p90) REVERT: L 241 MET cc_start: 0.7667 (mmm) cc_final: 0.7232 (mtp) REVERT: Q 14 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8635 (tt) REVERT: Q 48 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8345 (mtt90) REVERT: R 19 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8007 (ptmm) REVERT: R 63 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8870 (mtmm) REVERT: R 73 ASP cc_start: 0.8087 (t0) cc_final: 0.7260 (t0) REVERT: S 4 MET cc_start: 0.9183 (mmm) cc_final: 0.8981 (mmm) REVERT: S 24 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7627 (ttpp) REVERT: S 79 LYS cc_start: 0.6367 (mmmt) cc_final: 0.5757 (mmtm) REVERT: S 80 ILE cc_start: 0.6992 (mt) cc_final: 0.6601 (mm) REVERT: S 112 LYS cc_start: 0.6017 (tptt) cc_final: 0.5516 (tptt) outliers start: 101 outliers final: 83 residues processed: 664 average time/residue: 0.3550 time to fit residues: 362.7653 Evaluate side-chains 680 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 591 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain E residue 286 CYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 85 VAL 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 193 ILE 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 102 TYR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 156 VAL 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 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 55 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 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 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 190 CYS 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 N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain Q residue 14 LEU 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 Q residue 164 SER Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 55 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 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: 0.9980 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 198 optimal weight: 0.0770 chunk 273 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- 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 K 97 GLN M 199 GLN P 6 GLN P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 118 GLN H 227 ASN J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099156 restraints weight = 37734.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102991 restraints weight = 21240.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105521 restraints weight = 14841.253| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23238 Z= 0.114 Angle : 0.581 10.774 31754 Z= 0.291 Chirality : 0.044 0.159 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.489 24.332 3096 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.58 % Allowed : 22.23 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.15), residues: 2826 helix: -1.96 (0.48), residues: 112 sheet: -0.57 (0.18), residues: 796 loop : -0.83 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 171 HIS 0.003 0.001 HIS L 109 PHE 0.017 0.001 PHE E 169 TYR 0.026 0.002 TYR D 106 ARG 0.008 0.001 ARG N 68 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 534) hydrogen bonds : angle 5.08551 ( 1536) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.91031 ( 8) covalent geometry : bond 0.00274 (23234) covalent geometry : angle 0.58077 (31746) ********************** 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 696 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 607 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLN cc_start: 0.8672 (tp40) cc_final: 0.8445 (tm-30) REVERT: D 95 MET cc_start: 0.7628 (ttp) cc_final: 0.7285 (tmm) REVERT: D 230 MET cc_start: 0.7352 (ptp) cc_final: 0.6882 (ptp) REVERT: E 110 ASP cc_start: 0.9039 (t0) cc_final: 0.8750 (t0) REVERT: E 146 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7413 (mt) REVERT: E 162 LYS cc_start: 0.8981 (mttm) cc_final: 0.8699 (mtpp) REVERT: E 206 ASP cc_start: 0.8727 (t70) cc_final: 0.8261 (t0) REVERT: E 278 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8479 (m-40) REVERT: E 280 LYS cc_start: 0.8635 (tttt) cc_final: 0.8078 (tppt) REVERT: G 199 ASN cc_start: 0.8991 (t0) cc_final: 0.8521 (t0) REVERT: G 231 GLU cc_start: 0.8710 (pt0) cc_final: 0.8331 (pt0) REVERT: I 84 ASP cc_start: 0.8201 (t70) cc_final: 0.7979 (t0) REVERT: I 100 TYR cc_start: 0.6368 (t80) cc_final: 0.5960 (t80) REVERT: I 102 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6573 (p90) REVERT: I 241 MET cc_start: 0.7644 (mmm) cc_final: 0.7229 (mtp) REVERT: K 92 ARG cc_start: 0.8784 (ptp-110) cc_final: 0.8117 (mtp85) REVERT: K 226 MET cc_start: 0.8223 (mtt) cc_final: 0.7754 (mtp) REVERT: K 231 ASP cc_start: 0.8903 (t0) cc_final: 0.8699 (t0) REVERT: M 48 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7819 (mtt-85) REVERT: O 19 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7990 (ptmm) REVERT: O 73 ASP cc_start: 0.8062 (t0) cc_final: 0.7236 (t0) REVERT: P 24 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7668 (ttpp) REVERT: P 80 ILE cc_start: 0.6894 (mt) cc_final: 0.6492 (mm) REVERT: P 112 LYS cc_start: 0.6173 (tptt) cc_final: 0.5713 (tptt) REVERT: H 110 ASP cc_start: 0.9019 (t0) cc_final: 0.8717 (t0) REVERT: H 149 GLN cc_start: 0.8520 (tp40) cc_final: 0.8067 (tp40) REVERT: H 172 GLN cc_start: 0.8505 (mt0) cc_final: 0.8151 (pp30) REVERT: H 176 ASN cc_start: 0.8784 (m-40) cc_final: 0.8546 (p0) REVERT: H 183 MET cc_start: 0.8834 (ttm) cc_final: 0.8221 (ttm) REVERT: H 280 LYS cc_start: 0.8589 (tttt) cc_final: 0.8053 (tppt) REVERT: J 197 TYR cc_start: 0.8703 (t80) cc_final: 0.8362 (t80) REVERT: J 199 ASN cc_start: 0.9005 (t0) cc_final: 0.8298 (t0) REVERT: J 231 GLU cc_start: 0.8595 (pt0) cc_final: 0.8249 (pt0) REVERT: L 102 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6783 (p90) REVERT: L 241 MET cc_start: 0.7593 (mmm) cc_final: 0.7185 (mtp) REVERT: N 62 GLU cc_start: 0.8733 (mp0) cc_final: 0.8408 (mp0) REVERT: N 66 MET cc_start: 0.9209 (mmm) cc_final: 0.8890 (mmm) REVERT: N 92 ARG cc_start: 0.8784 (ptp-110) cc_final: 0.8131 (mtp85) REVERT: Q 48 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8102 (mmt90) REVERT: R 19 LYS cc_start: 0.8290 (ptmt) cc_final: 0.7903 (ptmm) REVERT: R 63 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8829 (mtmm) REVERT: R 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7247 (t0) REVERT: S 24 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7619 (ttpp) REVERT: S 79 LYS cc_start: 0.6279 (mmmt) cc_final: 0.5973 (tttm) REVERT: S 80 ILE cc_start: 0.6897 (mt) cc_final: 0.6487 (mm) REVERT: S 112 LYS cc_start: 0.6164 (tptt) cc_final: 0.5663 (tptt) outliers start: 89 outliers final: 71 residues processed: 658 average time/residue: 0.3598 time to fit residues: 365.8818 Evaluate side-chains 671 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 596 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 176 ASN Chi-restraints excluded: chain D residue 248 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 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain E residue 286 CYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 85 VAL 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 201 VAL 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 231 GLU Chi-restraints excluded: chain K residue 36 ILE 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 K residue 225 THR Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain O residue 55 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 7 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR 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 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 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 N residue 36 ILE Chi-restraints excluded: chain N residue 47 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 Q residue 215 VAL Chi-restraints excluded: chain R residue 55 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 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 189 GLN H 227 ASN J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097619 restraints weight = 37668.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101441 restraints weight = 21270.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103960 restraints weight = 14866.922| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.235 23238 Z= 0.201 Angle : 0.771 59.199 31754 Z= 0.452 Chirality : 0.046 0.778 3580 Planarity : 0.006 0.182 4038 Dihedral : 4.551 38.091 3096 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.46 % Allowed : 22.15 % Favored : 74.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.22 (0.15), residues: 2826 helix: -1.95 (0.48), residues: 112 sheet: -0.58 (0.18), residues: 796 loop : -0.83 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 171 HIS 0.003 0.001 HIS L 109 PHE 0.016 0.001 PHE E 169 TYR 0.024 0.002 TYR D 106 ARG 0.006 0.000 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 534) hydrogen bonds : angle 5.08391 ( 1536) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.69416 ( 8) covalent geometry : bond 0.00423 (23234) covalent geometry : angle 0.77029 (31746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10013.97 seconds wall clock time: 178 minutes 1.11 seconds (10681.11 seconds total)