Starting phenix.real_space_refine on Sun Sep 29 11:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_38171.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_38171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_38171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_38171.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x9b_38171/09_2024/8x9b_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.74, per 1000 atoms: 0.61 Number of scatterers: 22600 At special positions: 0 Unit cell: (193.76, 148.96, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 4136 8.00 N 3762 7.00 C 14562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 93 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 3.2 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: 3.20 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: 6.88 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3630 1.31 - 1.44: 6544 1.44 - 1.56: 12846 1.56 - 1.69: 2 1.69 - 1.81: 212 Bond restraints: 23234 Sorted by residual: bond pdb=" N PRO G 163 " pdb=" CD PRO G 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.88e+01 bond pdb=" N PRO J 163 " pdb=" CD PRO J 163 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.79e+01 bond pdb=" CA LEU L 172 " pdb=" C LEU L 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA LEU I 172 " pdb=" C LEU I 172 " ideal model delta sigma weight residual 1.522 1.438 0.085 1.36e-02 5.41e+03 3.88e+01 bond pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.19e-02 7.06e+03 3.67e+01 ... (remaining 23229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 30296 3.31 - 6.62: 1257 6.62 - 9.93: 141 9.93 - 13.24: 34 13.24 - 16.55: 18 Bond angle restraints: 31746 Sorted by residual: angle pdb=" N ALA O 101 " pdb=" CA ALA O 101 " pdb=" C ALA O 101 " ideal model delta sigma weight residual 111.36 127.05 -15.69 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N ALA R 101 " pdb=" CA ALA R 101 " pdb=" C ALA R 101 " ideal model delta sigma weight residual 111.36 127.03 -15.67 1.09e+00 8.42e-01 2.07e+02 angle pdb=" N HIS L 145 " pdb=" CA HIS L 145 " pdb=" C HIS L 145 " ideal model delta sigma weight residual 108.13 95.41 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" N HIS I 145 " pdb=" CA HIS I 145 " pdb=" C HIS I 145 " ideal model delta sigma weight residual 108.13 95.42 12.71 9.00e-01 1.23e+00 1.99e+02 angle pdb=" N PHE G 82 " pdb=" CA PHE G 82 " pdb=" C PHE G 82 " ideal model delta sigma weight residual 112.35 128.90 -16.55 1.34e+00 5.57e-01 1.52e+02 ... (remaining 31741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 12666 17.30 - 34.60: 808 34.60 - 51.90: 120 51.90 - 69.20: 36 69.20 - 86.50: 20 Dihedral angle restraints: 13650 sinusoidal: 5280 harmonic: 8370 Sorted by residual: dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 93 " pdb=" CB CYS P 93 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CA PHE G 82 " pdb=" CB PHE G 82 " ideal model delta harmonic sigma weight residual 122.80 133.63 -10.83 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" N PHE J 82 " pdb=" C PHE J 82 " pdb=" CA PHE J 82 " pdb=" CB PHE J 82 " ideal model delta harmonic sigma weight residual 122.80 133.57 -10.77 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 13647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3054 0.136 - 0.272: 477 0.272 - 0.409: 41 0.409 - 0.545: 6 0.545 - 0.681: 2 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CA PHE G 82 " pdb=" N PHE G 82 " pdb=" C PHE G 82 " pdb=" CB PHE G 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE J 82 " pdb=" N PHE J 82 " pdb=" C PHE J 82 " pdb=" CB PHE J 82 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TRP F 261 " pdb=" N TRP F 261 " pdb=" C TRP F 261 " pdb=" CB TRP F 261 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 3577 not shown) Planarity restraints: 4038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR P 36 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR P 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR P 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR P 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR S 36 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR S 36 " -0.068 2.00e-02 2.50e+03 pdb=" O THR S 36 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR S 37 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 186 " 0.331 9.50e-02 1.11e+02 1.48e-01 1.36e+01 pdb=" NE ARG I 186 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG I 186 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG I 186 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 186 " 0.010 2.00e-02 2.50e+03 ... (remaining 4035 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 350 2.60 - 3.18: 18318 3.18 - 3.75: 31514 3.75 - 4.33: 43271 4.33 - 4.90: 73984 Nonbonded interactions: 167437 Sorted by model distance: nonbonded pdb=" SG CYS R 22 " pdb=" SG CYS R 96 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS S 23 " pdb=" SG CYS S 93 " model vdw 2.061 3.760 nonbonded pdb=" N ALA I 168 " pdb=" O ALA I 168 " model vdw 2.173 2.496 nonbonded pdb=" N ALA L 168 " pdb=" O ALA L 168 " model vdw 2.174 2.496 nonbonded pdb=" N TRP O 104 " pdb=" O TRP O 104 " model vdw 2.267 2.496 ... (remaining 167432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 74 through 209 or resid 223 through 297)) selection = chain 'F' selection = (chain 'H' and (resid 74 through 209 or resid 223 through 297)) } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'K' and resid 11 through 232) selection = chain 'M' selection = (chain 'N' and resid 11 through 232) selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.140 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.139 23234 Z= 0.783 Angle : 1.572 16.548 31746 Z= 1.020 Chirality : 0.100 0.681 3580 Planarity : 0.011 0.148 4038 Dihedral : 12.253 86.504 8260 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 2826 helix: -3.17 (0.40), residues: 124 sheet: -1.62 (0.17), residues: 844 loop : -2.19 (0.12), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP S 40 HIS 0.006 0.001 HIS I 118 PHE 0.024 0.003 PHE D 84 TYR 0.022 0.003 TYR N 107 ARG 0.017 0.002 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1009 time to evaluate : 2.705 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: 0.3915 time to fit residues: 592.8433 Evaluate side-chains 701 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 189 GLN D 269 GLN E 227 ASN E 269 GLN G 118 HIS G 152 GLN G 225 ASN I 145 HIS I 174 GLN I 209 HIS K 12 GLN K 61 ASN K 97 GLN M 174 ASN O 57 ASN P 6 GLN P 43 GLN F 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 189 GLN F 269 GLN ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN H 228 ASN H 269 GLN J 118 HIS J 152 GLN J 225 ASN L 145 HIS L 155 GLN L 174 GLN L 209 HIS N 12 GLN N 61 ASN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 ASN R 57 ASN S 6 GLN S 43 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23234 Z= 0.281 Angle : 0.673 10.104 31746 Z= 0.349 Chirality : 0.048 0.192 3580 Planarity : 0.006 0.063 4038 Dihedral : 5.145 27.949 3096 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.58 % Allowed : 13.83 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 2826 helix: -3.42 (0.32), residues: 122 sheet: -1.14 (0.17), residues: 808 loop : -1.67 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 171 HIS 0.006 0.001 HIS I 145 PHE 0.025 0.002 PHE R 27 TYR 0.026 0.002 TYR P 92 ARG 0.008 0.001 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 716 time to evaluate : 2.549 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: 0.8902 (tp40) cc_final: 0.8593 (tp-100) REVERT: D 143 ASN cc_start: 0.8918 (p0) cc_final: 0.8453 (p0) REVERT: D 205 TYR cc_start: 0.8114 (t80) cc_final: 0.7838 (t80) REVERT: D 278 ASN cc_start: 0.8503 (m110) cc_final: 0.8297 (m110) REVERT: D 279 TYR cc_start: 0.8663 (p90) cc_final: 0.8206 (p90) REVERT: E 106 TYR cc_start: 0.8754 (p90) cc_final: 0.8519 (p90) REVERT: E 119 LEU cc_start: 0.8568 (tp) cc_final: 0.8333 (tp) REVERT: E 147 VAL cc_start: 0.8463 (t) cc_final: 0.8008 (p) REVERT: E 149 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7866 (tp40) REVERT: E 183 MET cc_start: 0.8870 (ttm) cc_final: 0.8410 (ttm) REVERT: G 30 ASN cc_start: 0.8144 (m-40) cc_final: 0.7866 (t0) REVERT: G 62 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7213 (mmm160) REVERT: G 74 ASP cc_start: 0.7401 (p0) cc_final: 0.7170 (p0) REVERT: G 104 SER cc_start: 0.8984 (t) cc_final: 0.8704 (m) REVERT: G 127 LEU cc_start: 0.8494 (tp) cc_final: 0.8122 (tp) REVERT: G 130 TYR cc_start: 0.8845 (t80) cc_final: 0.8549 (t80) REVERT: G 164 TYR cc_start: 0.9188 (t80) cc_final: 0.8820 (t80) REVERT: G 199 ASN cc_start: 0.8898 (t0) cc_final: 0.8637 (t0) REVERT: G 231 GLU cc_start: 0.8592 (pt0) cc_final: 0.8347 (pt0) REVERT: I 30 ASN cc_start: 0.7463 (m-40) cc_final: 0.6968 (p0) REVERT: I 76 LYS cc_start: 0.8878 (mttt) cc_final: 0.8514 (mtpp) REVERT: I 84 ASP cc_start: 0.8146 (t70) cc_final: 0.7842 (t0) REVERT: I 209 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8245 (t70) REVERT: I 223 ASP cc_start: 0.8732 (t0) cc_final: 0.8442 (m-30) REVERT: K 28 PHE cc_start: 0.8258 (t80) cc_final: 0.7799 (t80) REVERT: K 78 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8398 (mmmt) REVERT: K 213 TYR cc_start: 0.8871 (m-80) cc_final: 0.8614 (m-80) REVERT: K 226 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: M 74 SER cc_start: 0.8714 (t) cc_final: 0.8501 (p) REVERT: O 3 GLN cc_start: 0.7846 (pt0) cc_final: 0.7221 (pm20) REVERT: O 5 VAL cc_start: 0.8020 (m) cc_final: 0.7774 (m) REVERT: O 19 LYS cc_start: 0.6843 (ptmt) cc_final: 0.6623 (ptmm) REVERT: O 22 CYS cc_start: 0.6264 (t) cc_final: 0.5757 (t) REVERT: P 54 TYR cc_start: 0.6974 (t80) cc_final: 0.6767 (t80) REVERT: P 97 THR cc_start: 0.7594 (m) cc_final: 0.7391 (p) REVERT: F 76 GLN cc_start: 0.8827 (tp40) cc_final: 0.8470 (tp-100) REVERT: F 143 ASN cc_start: 0.8824 (p0) cc_final: 0.8459 (p0) REVERT: F 205 TYR cc_start: 0.8098 (t80) cc_final: 0.7815 (t80) REVERT: F 279 TYR cc_start: 0.8802 (p90) cc_final: 0.8568 (p90) REVERT: H 147 VAL cc_start: 0.8422 (t) cc_final: 0.8046 (p) REVERT: H 154 MET cc_start: 0.8318 (ttp) cc_final: 0.8107 (ttm) REVERT: H 183 MET cc_start: 0.8935 (ttm) cc_final: 0.8366 (ttm) REVERT: J 127 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8281 (tp) REVERT: J 164 TYR cc_start: 0.9207 (t80) cc_final: 0.8907 (t80) REVERT: J 199 ASN cc_start: 0.8949 (t0) cc_final: 0.8656 (t0) REVERT: J 231 GLU cc_start: 0.8522 (pt0) cc_final: 0.8285 (pt0) REVERT: L 30 ASN cc_start: 0.7486 (m-40) cc_final: 0.7015 (p0) REVERT: L 76 LYS cc_start: 0.8850 (mttt) cc_final: 0.8439 (mtpp) REVERT: L 84 ASP cc_start: 0.8198 (t70) cc_final: 0.7793 (t0) REVERT: N 67 GLN cc_start: 0.9302 (mt0) cc_final: 0.9094 (mt0) REVERT: N 78 LYS cc_start: 0.8732 (mptt) cc_final: 0.8440 (mmmt) REVERT: Q 78 LYS cc_start: 0.7851 (tmtt) cc_final: 0.7557 (tmtt) REVERT: R 3 GLN cc_start: 0.7844 (pt0) cc_final: 0.7193 (pm20) REVERT: R 19 LYS cc_start: 0.6824 (ptmt) cc_final: 0.6603 (ptmm) REVERT: R 22 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.6942 (p) REVERT: R 28 ASN cc_start: 0.8970 (t0) cc_final: 0.8746 (t0) REVERT: S 54 TYR cc_start: 0.7016 (t80) cc_final: 0.6786 (t80) REVERT: S 80 ILE cc_start: 0.6159 (mt) cc_final: 0.5868 (mm) outliers start: 89 outliers final: 54 residues processed: 757 average time/residue: 0.3668 time to fit residues: 425.1621 Evaluate side-chains 704 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 646 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 286 CYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 226 MET Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 286 CYS Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 116 GLU Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 214 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 279 optimal weight: 0.0870 chunk 230 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 245 HIS E 227 ASN G 152 GLN I 145 HIS I 208 ASN I 209 HIS K 12 GLN K 29 HIS ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN H 118 GLN H 227 ASN H 276 ASN J 152 GLN J 211 ASN L 145 HIS L 209 HIS ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 GLN ** Q 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23234 Z= 0.189 Angle : 0.592 8.659 31746 Z= 0.300 Chirality : 0.045 0.189 3580 Planarity : 0.005 0.054 4038 Dihedral : 4.754 26.371 3096 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.14 % Allowed : 16.36 % Favored : 79.50 % 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: -3.17 (0.36), residues: 120 sheet: -0.86 (0.17), residues: 836 loop : -1.32 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 171 HIS 0.009 0.001 HIS I 209 PHE 0.025 0.001 PHE O 27 TYR 0.019 0.001 TYR H 106 ARG 0.005 0.001 ARG E 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 677 time to evaluate : 2.712 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: 0.8671 (tp40) cc_final: 0.7950 (tm-30) REVERT: D 82 ASN cc_start: 0.8703 (m110) cc_final: 0.7945 (m-40) REVERT: D 185 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (t0) REVERT: E 147 VAL cc_start: 0.8644 (t) cc_final: 0.8399 (p) REVERT: E 162 LYS cc_start: 0.8848 (mttm) cc_final: 0.8496 (mtpp) REVERT: E 183 MET cc_start: 0.8933 (ttm) cc_final: 0.8618 (ttm) REVERT: G 30 ASN cc_start: 0.8120 (m-40) cc_final: 0.7908 (t0) REVERT: G 104 SER cc_start: 0.8999 (t) cc_final: 0.8565 (m) REVERT: G 127 LEU cc_start: 0.8526 (tp) cc_final: 0.8181 (tp) REVERT: G 199 ASN cc_start: 0.9013 (t0) cc_final: 0.8637 (t0) REVERT: G 231 GLU cc_start: 0.8534 (pt0) cc_final: 0.8262 (pt0) REVERT: I 30 ASN cc_start: 0.7344 (m-40) cc_final: 0.6982 (p0) REVERT: I 76 LYS cc_start: 0.8804 (mttt) cc_final: 0.8394 (mtpp) REVERT: I 84 ASP cc_start: 0.8166 (t70) cc_final: 0.7770 (t0) REVERT: K 78 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8563 (mmmt) REVERT: K 226 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: M 74 SER cc_start: 0.8716 (t) cc_final: 0.8503 (p) REVERT: O 3 GLN cc_start: 0.7896 (pt0) cc_final: 0.7266 (pm20) REVERT: O 5 VAL cc_start: 0.7995 (m) cc_final: 0.7787 (m) REVERT: O 19 LYS cc_start: 0.6878 (ptmt) cc_final: 0.6644 (ptmm) REVERT: O 63 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8028 (mtmm) REVERT: P 54 TYR cc_start: 0.6924 (t80) cc_final: 0.6676 (t80) REVERT: F 76 GLN cc_start: 0.8816 (tp40) cc_final: 0.8566 (tp-100) REVERT: F 95 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7634 (mmm) REVERT: F 185 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7950 (t0) REVERT: H 149 GLN cc_start: 0.8362 (tp40) cc_final: 0.8003 (tp40) REVERT: H 162 LYS cc_start: 0.8865 (mttm) cc_final: 0.8511 (mtpp) REVERT: H 183 MET cc_start: 0.8893 (ttm) cc_final: 0.8691 (ttm) REVERT: H 275 THR cc_start: 0.8940 (p) cc_final: 0.8664 (t) REVERT: J 30 ASN cc_start: 0.8159 (m-40) cc_final: 0.7939 (t0) REVERT: J 74 ASP cc_start: 0.7473 (p0) cc_final: 0.7216 (p0) REVERT: J 79 TYR cc_start: 0.8888 (p90) cc_final: 0.8629 (p90) REVERT: J 81 LYS cc_start: 0.8749 (mttm) cc_final: 0.8522 (mttm) REVERT: J 199 ASN cc_start: 0.9019 (t0) cc_final: 0.8588 (t0) REVERT: L 30 ASN cc_start: 0.7361 (m-40) cc_final: 0.7017 (p0) REVERT: L 76 LYS cc_start: 0.8756 (mttt) cc_final: 0.8361 (mtpp) REVERT: L 84 ASP cc_start: 0.8205 (t70) cc_final: 0.7820 (t0) REVERT: N 78 LYS cc_start: 0.8755 (mptt) cc_final: 0.8448 (mmmt) REVERT: Q 48 ARG cc_start: 0.8591 (mtt90) cc_final: 0.8234 (mtt-85) REVERT: R 3 GLN cc_start: 0.7905 (pt0) cc_final: 0.7267 (pm20) REVERT: R 19 LYS cc_start: 0.6820 (ptmt) cc_final: 0.6603 (ptmm) REVERT: R 22 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.6957 (p) REVERT: R 63 LYS cc_start: 0.8265 (mtmt) cc_final: 0.8051 (mtmm) REVERT: S 54 TYR cc_start: 0.7019 (t80) cc_final: 0.6663 (t80) REVERT: S 80 ILE cc_start: 0.6008 (mt) cc_final: 0.5756 (mm) REVERT: S 108 LYS cc_start: 0.7381 (mttt) cc_final: 0.7059 (tptt) outliers start: 103 outliers final: 77 residues processed: 725 average time/residue: 0.3556 time to fit residues: 390.8193 Evaluate side-chains 717 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 635 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain I residue 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 209 HIS Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 226 MET Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 38 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 164 SER Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 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 82 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN J 152 GLN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 HIS L 208 ASN N 61 ASN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23234 Z= 0.277 Angle : 0.604 8.401 31746 Z= 0.307 Chirality : 0.046 0.239 3580 Planarity : 0.005 0.107 4038 Dihedral : 4.794 25.198 3096 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.35 % Allowed : 16.72 % Favored : 77.93 % 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: -1.69 (0.15), residues: 2826 helix: -3.10 (0.36), residues: 122 sheet: -0.71 (0.17), residues: 836 loop : -1.19 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP E 171 HIS 0.010 0.001 HIS I 209 PHE 0.024 0.002 PHE R 27 TYR 0.022 0.002 TYR F 106 ARG 0.007 0.000 ARG E 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 648 time to evaluate : 2.727 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: D 76 GLN cc_start: 0.8703 (tp40) cc_final: 0.8127 (tm-30) REVERT: D 82 ASN cc_start: 0.8800 (m110) cc_final: 0.8182 (m-40) REVERT: D 271 TYR cc_start: 0.8645 (m-80) cc_final: 0.8363 (m-80) REVERT: E 149 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8225 (tp-100) REVERT: E 162 LYS cc_start: 0.8909 (mttm) cc_final: 0.8595 (mtpp) REVERT: E 206 ASP cc_start: 0.8672 (t0) cc_final: 0.8426 (t0) REVERT: G 30 ASN cc_start: 0.8318 (m-40) cc_final: 0.8013 (t0) REVERT: G 127 LEU cc_start: 0.8594 (tp) cc_final: 0.8354 (tp) REVERT: G 199 ASN cc_start: 0.9109 (t0) cc_final: 0.8675 (t0) REVERT: I 30 ASN cc_start: 0.7353 (m-40) cc_final: 0.6954 (p0) REVERT: I 76 LYS cc_start: 0.8837 (mttt) cc_final: 0.8444 (mtpp) REVERT: I 84 ASP cc_start: 0.8295 (t70) cc_final: 0.7931 (t0) REVERT: K 78 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8661 (mmmt) REVERT: K 226 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7731 (mtt) REVERT: M 48 ARG cc_start: 0.8696 (mtt90) cc_final: 0.8472 (mtt90) REVERT: O 3 GLN cc_start: 0.7936 (pt0) cc_final: 0.7307 (pm20) REVERT: O 19 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6699 (ptmm) REVERT: O 63 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7989 (mtmm) REVERT: P 54 TYR cc_start: 0.7007 (t80) cc_final: 0.6764 (t80) REVERT: P 80 ILE cc_start: 0.6002 (mt) cc_final: 0.5752 (mm) REVERT: P 108 LYS cc_start: 0.7471 (mttt) cc_final: 0.7166 (tptt) REVERT: F 76 GLN cc_start: 0.8824 (tp40) cc_final: 0.8379 (tm-30) REVERT: F 82 ASN cc_start: 0.8723 (m110) cc_final: 0.8367 (m-40) REVERT: F 95 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: H 149 GLN cc_start: 0.8506 (tp40) cc_final: 0.8264 (tp-100) REVERT: H 275 THR cc_start: 0.8960 (p) cc_final: 0.8657 (t) REVERT: J 30 ASN cc_start: 0.8186 (m-40) cc_final: 0.7886 (t0) REVERT: J 104 SER cc_start: 0.9083 (t) cc_final: 0.8605 (m) REVERT: J 192 THR cc_start: 0.8515 (m) cc_final: 0.8251 (t) REVERT: J 199 ASN cc_start: 0.9034 (t0) cc_final: 0.8536 (t0) REVERT: L 30 ASN cc_start: 0.7375 (m-40) cc_final: 0.7006 (p0) REVERT: L 76 LYS cc_start: 0.8786 (mttt) cc_final: 0.8443 (mtpp) REVERT: L 84 ASP cc_start: 0.8268 (t70) cc_final: 0.7984 (t0) REVERT: N 62 GLU cc_start: 0.8613 (mp0) cc_final: 0.8409 (mp0) REVERT: N 78 LYS cc_start: 0.8722 (mptt) cc_final: 0.8486 (mmmt) REVERT: Q 48 ARG cc_start: 0.8626 (mtt90) cc_final: 0.8391 (mmt90) REVERT: Q 67 GLN cc_start: 0.8955 (mt0) cc_final: 0.8722 (mt0) REVERT: Q 108 TYR cc_start: 0.9223 (m-80) cc_final: 0.8936 (m-80) REVERT: R 3 GLN cc_start: 0.7948 (pt0) cc_final: 0.7334 (pm20) REVERT: R 19 LYS cc_start: 0.6921 (ptmt) cc_final: 0.6623 (ptmm) REVERT: R 22 CYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7224 (p) REVERT: R 63 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8034 (mtmm) REVERT: R 95 TYR cc_start: 0.6412 (m-80) cc_final: 0.6055 (m-80) REVERT: S 54 TYR cc_start: 0.7018 (t80) cc_final: 0.6714 (t80) REVERT: S 80 ILE cc_start: 0.5915 (mt) cc_final: 0.5569 (mm) REVERT: S 108 LYS cc_start: 0.7361 (mttt) cc_final: 0.7064 (tptt) outliers start: 133 outliers final: 98 residues processed: 718 average time/residue: 0.3508 time to fit residues: 383.1359 Evaluate side-chains 725 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 624 time to evaluate : 2.601 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 248 THR 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 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 87 THR 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 208 ASN Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 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 58 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 143 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 132 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 115 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain 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 22 CYS Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 33 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 2.9990 chunk 155 optimal weight: 0.0870 chunk 3 optimal weight: 0.0770 chunk 204 optimal weight: 0.1980 chunk 113 optimal weight: 20.0000 chunk 234 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.8518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN G 225 ASN I 209 HIS ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 202 GLN F 245 HIS H 118 GLN H 227 ASN J 152 GLN L 145 HIS L 155 GLN L 209 HIS ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 GLN S 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23234 Z= 0.143 Angle : 0.550 7.923 31746 Z= 0.275 Chirality : 0.044 0.220 3580 Planarity : 0.005 0.054 4038 Dihedral : 4.481 23.427 3096 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.22 % Allowed : 19.21 % Favored : 76.57 % 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: -1.47 (0.15), residues: 2826 helix: -2.97 (0.36), residues: 124 sheet: -0.60 (0.17), residues: 834 loop : -1.02 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 171 HIS 0.004 0.001 HIS F 245 PHE 0.024 0.001 PHE K 28 TYR 0.023 0.001 TYR D 106 ARG 0.013 0.000 ARG F 254 *********************** 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 753 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 648 time to evaluate : 2.456 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: D 76 GLN cc_start: 0.8730 (tp40) cc_final: 0.8257 (tm-30) REVERT: D 82 ASN cc_start: 0.8823 (m110) cc_final: 0.8368 (m-40) REVERT: E 149 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8264 (tp-100) REVERT: E 162 LYS cc_start: 0.8894 (mttm) cc_final: 0.8618 (mtpp) REVERT: E 183 MET cc_start: 0.8836 (ttm) cc_final: 0.8529 (ttm) REVERT: G 30 ASN cc_start: 0.8251 (m-40) cc_final: 0.7928 (t0) REVERT: G 127 LEU cc_start: 0.8546 (tp) cc_final: 0.8268 (tp) REVERT: G 199 ASN cc_start: 0.9097 (t0) cc_final: 0.8623 (t0) REVERT: I 30 ASN cc_start: 0.7302 (m-40) cc_final: 0.6996 (p0) REVERT: I 76 LYS cc_start: 0.8711 (mttt) cc_final: 0.8307 (mtpp) REVERT: I 84 ASP cc_start: 0.8143 (t70) cc_final: 0.7723 (t0) REVERT: K 62 GLU cc_start: 0.8663 (mp0) cc_final: 0.8243 (mp0) REVERT: K 78 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8724 (mmmt) REVERT: K 226 MET cc_start: 0.8078 (mtt) cc_final: 0.7756 (mtt) REVERT: M 48 ARG cc_start: 0.8642 (mtt90) cc_final: 0.8150 (mtt-85) REVERT: O 3 GLN cc_start: 0.7985 (pt0) cc_final: 0.7360 (pm20) REVERT: O 19 LYS cc_start: 0.6863 (ptmt) cc_final: 0.6640 (ptmt) REVERT: O 63 LYS cc_start: 0.8362 (mtmt) cc_final: 0.8020 (mtmm) REVERT: O 95 TYR cc_start: 0.6462 (m-80) cc_final: 0.6103 (m-80) REVERT: P 4 MET cc_start: 0.8610 (mmm) cc_final: 0.8114 (mmm) REVERT: P 54 TYR cc_start: 0.6986 (t80) cc_final: 0.6765 (t80) REVERT: P 80 ILE cc_start: 0.5880 (mt) cc_final: 0.5589 (mm) REVERT: P 108 LYS cc_start: 0.7419 (mttt) cc_final: 0.7128 (tptt) REVERT: F 76 GLN cc_start: 0.8772 (tp40) cc_final: 0.8243 (tm-30) REVERT: F 82 ASN cc_start: 0.8686 (m110) cc_final: 0.8254 (m-40) REVERT: H 118 GLN cc_start: 0.8654 (tp40) cc_final: 0.8331 (tp-100) REVERT: H 149 GLN cc_start: 0.8458 (tp40) cc_final: 0.8214 (tp-100) REVERT: H 183 MET cc_start: 0.8764 (ttm) cc_final: 0.8414 (ttm) REVERT: H 275 THR cc_start: 0.8910 (p) cc_final: 0.8614 (t) REVERT: J 30 ASN cc_start: 0.8199 (m-40) cc_final: 0.7964 (t0) REVERT: J 199 ASN cc_start: 0.9102 (t0) cc_final: 0.8545 (t0) REVERT: L 30 ASN cc_start: 0.7334 (m-40) cc_final: 0.7040 (p0) REVERT: L 76 LYS cc_start: 0.8695 (mttt) cc_final: 0.8287 (mtpp) REVERT: L 84 ASP cc_start: 0.8118 (t70) cc_final: 0.7836 (t0) REVERT: N 62 GLU cc_start: 0.8634 (mp0) cc_final: 0.8344 (mp0) REVERT: Q 108 TYR cc_start: 0.9155 (m-80) cc_final: 0.8797 (m-80) REVERT: R 3 GLN cc_start: 0.7946 (pt0) cc_final: 0.7326 (pm20) REVERT: R 19 LYS cc_start: 0.6779 (ptmt) cc_final: 0.6578 (ptmt) REVERT: R 22 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7262 (p) REVERT: R 59 MET cc_start: 0.6503 (ttt) cc_final: 0.6244 (ttp) REVERT: R 63 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8101 (mtmm) REVERT: R 95 TYR cc_start: 0.6333 (m-80) cc_final: 0.6034 (m-80) REVERT: S 4 MET cc_start: 0.8540 (mmm) cc_final: 0.8114 (mmm) REVERT: S 54 TYR cc_start: 0.7007 (t80) cc_final: 0.6556 (t80) REVERT: S 80 ILE cc_start: 0.5791 (mt) cc_final: 0.5473 (mm) REVERT: S 108 LYS cc_start: 0.7349 (mttt) cc_final: 0.7125 (tptt) outliers start: 105 outliers final: 72 residues processed: 705 average time/residue: 0.3503 time to fit residues: 377.9528 Evaluate side-chains 694 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 621 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 185 ASP 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 247 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain 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 208 ASN Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 164 SER 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 164 SER Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 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 185 ASP Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 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 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 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 204 VAL Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.7980 chunk 247 optimal weight: 0.0270 chunk 54 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 274 optimal weight: 0.0030 chunk 228 optimal weight: 0.0010 chunk 127 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 245 HIS H 227 ASN J 109 HIS J 152 GLN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23234 Z= 0.138 Angle : 0.535 7.364 31746 Z= 0.269 Chirality : 0.043 0.225 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.294 23.325 3096 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.82 % Allowed : 20.10 % Favored : 76.09 % 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: -2.70 (0.38), residues: 124 sheet: -0.46 (0.17), residues: 828 loop : -0.91 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 171 HIS 0.012 0.001 HIS L 145 PHE 0.028 0.001 PHE O 27 TYR 0.025 0.001 TYR F 106 ARG 0.011 0.000 ARG F 254 *********************** 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 742 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 647 time to evaluate : 2.578 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: D 76 GLN cc_start: 0.8706 (tp40) cc_final: 0.8303 (tm-30) REVERT: D 82 ASN cc_start: 0.8764 (m110) cc_final: 0.8328 (m-40) REVERT: E 119 LEU cc_start: 0.8557 (tp) cc_final: 0.8244 (tp) REVERT: E 128 TYR cc_start: 0.9372 (m-80) cc_final: 0.9072 (m-10) REVERT: E 149 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8324 (tp-100) REVERT: E 162 LYS cc_start: 0.8920 (mttm) cc_final: 0.8627 (mtpp) REVERT: E 183 MET cc_start: 0.8833 (ttm) cc_final: 0.8548 (ttm) REVERT: E 278 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: G 30 ASN cc_start: 0.8254 (m-40) cc_final: 0.7912 (t0) REVERT: G 127 LEU cc_start: 0.8625 (tp) cc_final: 0.8362 (tp) REVERT: G 199 ASN cc_start: 0.9090 (t0) cc_final: 0.8569 (t0) REVERT: G 231 GLU cc_start: 0.8641 (pt0) cc_final: 0.8361 (pt0) REVERT: I 30 ASN cc_start: 0.7291 (m-40) cc_final: 0.7034 (p0) REVERT: I 76 LYS cc_start: 0.8650 (mttt) cc_final: 0.8258 (mtpp) REVERT: I 84 ASP cc_start: 0.8048 (t70) cc_final: 0.7607 (t0) REVERT: I 152 GLN cc_start: 0.8683 (mm110) cc_final: 0.8480 (mm110) REVERT: K 62 GLU cc_start: 0.8635 (mp0) cc_final: 0.8165 (mp0) REVERT: K 226 MET cc_start: 0.8156 (mtt) cc_final: 0.7813 (mtp) REVERT: M 48 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8204 (mtt-85) REVERT: O 3 GLN cc_start: 0.7991 (pt0) cc_final: 0.7362 (pm20) REVERT: O 63 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8051 (mtmm) REVERT: O 95 TYR cc_start: 0.6317 (m-80) cc_final: 0.6042 (m-80) REVERT: O 98 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.5597 (ptt90) REVERT: P 54 TYR cc_start: 0.7002 (t80) cc_final: 0.6754 (t80) REVERT: P 80 ILE cc_start: 0.5808 (mt) cc_final: 0.5525 (mm) REVERT: P 108 LYS cc_start: 0.7392 (mttt) cc_final: 0.7111 (tptt) REVERT: F 76 GLN cc_start: 0.8731 (tp40) cc_final: 0.8302 (tm-30) REVERT: F 82 ASN cc_start: 0.8667 (m110) cc_final: 0.8299 (m-40) REVERT: F 95 MET cc_start: 0.7761 (mmm) cc_final: 0.7400 (mmm) REVERT: H 118 GLN cc_start: 0.8631 (tp40) cc_final: 0.8303 (tp-100) REVERT: H 149 GLN cc_start: 0.8400 (tp40) cc_final: 0.8185 (tp-100) REVERT: H 176 ASN cc_start: 0.8893 (m-40) cc_final: 0.8093 (p0) REVERT: H 183 MET cc_start: 0.8795 (ttm) cc_final: 0.8435 (ttm) REVERT: J 30 ASN cc_start: 0.8195 (m-40) cc_final: 0.7973 (t0) REVERT: J 199 ASN cc_start: 0.9094 (t0) cc_final: 0.8520 (t0) REVERT: J 231 GLU cc_start: 0.8548 (pt0) cc_final: 0.8289 (pt0) REVERT: L 30 ASN cc_start: 0.7328 (m-40) cc_final: 0.7064 (p0) REVERT: L 76 LYS cc_start: 0.8627 (mttt) cc_final: 0.8236 (mtpp) REVERT: L 84 ASP cc_start: 0.8099 (t70) cc_final: 0.7780 (t0) REVERT: N 62 GLU cc_start: 0.8626 (mp0) cc_final: 0.8304 (mp0) REVERT: Q 48 ARG cc_start: 0.8678 (mtt90) cc_final: 0.8280 (mtt-85) REVERT: Q 108 TYR cc_start: 0.9113 (m-80) cc_final: 0.8756 (m-80) REVERT: R 3 GLN cc_start: 0.7948 (pt0) cc_final: 0.7322 (pm20) REVERT: R 22 CYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7278 (p) REVERT: R 63 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8040 (mtmm) REVERT: R 95 TYR cc_start: 0.6190 (m-80) cc_final: 0.5883 (m-80) REVERT: S 54 TYR cc_start: 0.6917 (t80) cc_final: 0.6630 (t80) REVERT: S 80 ILE cc_start: 0.5742 (mt) cc_final: 0.5420 (mm) outliers start: 95 outliers final: 67 residues processed: 699 average time/residue: 0.3446 time to fit residues: 366.6555 Evaluate side-chains 700 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 630 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 185 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 CYS 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 208 ASN 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 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 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 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 185 ASP Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE 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 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 81 GLU Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 225 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 38 VAL 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 264 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 273 optimal weight: 0.2980 chunk 171 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 126 optimal weight: 4.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 199 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 245 HIS H 227 ASN J 109 HIS J 152 GLN L 145 HIS N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN S 105 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23234 Z= 0.173 Angle : 0.547 8.060 31746 Z= 0.273 Chirality : 0.044 0.188 3580 Planarity : 0.004 0.050 4038 Dihedral : 4.256 22.673 3096 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.94 % Allowed : 20.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 2826 helix: -2.38 (0.41), residues: 122 sheet: -0.45 (0.17), residues: 838 loop : -0.83 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 203 HIS 0.004 0.001 HIS F 245 PHE 0.028 0.001 PHE R 27 TYR 0.025 0.001 TYR F 106 ARG 0.009 0.000 ARG F 254 *********************** 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 742 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 644 time to evaluate : 2.574 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: D 76 GLN cc_start: 0.8706 (tp40) cc_final: 0.8345 (tm-30) REVERT: D 82 ASN cc_start: 0.8737 (m110) cc_final: 0.8348 (m-40) REVERT: E 119 LEU cc_start: 0.8582 (tp) cc_final: 0.8264 (tp) REVERT: E 128 TYR cc_start: 0.9362 (m-80) cc_final: 0.9035 (m-10) REVERT: E 149 GLN cc_start: 0.8491 (tp40) cc_final: 0.8227 (tp-100) REVERT: E 162 LYS cc_start: 0.8923 (mttm) cc_final: 0.8628 (mtpp) REVERT: E 183 MET cc_start: 0.8811 (ttm) cc_final: 0.8515 (ttm) REVERT: E 278 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: G 30 ASN cc_start: 0.8272 (m-40) cc_final: 0.7882 (t0) REVERT: G 103 ARG cc_start: 0.8415 (ptm160) cc_final: 0.8095 (ptm160) REVERT: G 127 LEU cc_start: 0.8665 (tp) cc_final: 0.8379 (tp) REVERT: G 199 ASN cc_start: 0.9074 (t0) cc_final: 0.8523 (t0) REVERT: G 231 GLU cc_start: 0.8666 (pt0) cc_final: 0.8355 (pt0) REVERT: I 30 ASN cc_start: 0.7324 (m-40) cc_final: 0.7019 (p0) REVERT: I 76 LYS cc_start: 0.8690 (mttt) cc_final: 0.8330 (mtpp) REVERT: I 84 ASP cc_start: 0.8084 (t70) cc_final: 0.7741 (t0) REVERT: K 62 GLU cc_start: 0.8685 (mp0) cc_final: 0.8255 (mp0) REVERT: K 92 ARG cc_start: 0.8879 (ptp-110) cc_final: 0.8263 (mtp85) REVERT: K 226 MET cc_start: 0.8165 (mtt) cc_final: 0.7854 (mtp) REVERT: M 48 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8202 (mtt-85) REVERT: O 3 GLN cc_start: 0.7969 (pt0) cc_final: 0.7381 (pm20) REVERT: O 63 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8083 (mtmm) REVERT: O 73 ASP cc_start: 0.5978 (t0) cc_final: 0.5462 (t0) REVERT: O 95 TYR cc_start: 0.6495 (m-80) cc_final: 0.6184 (m-80) REVERT: O 98 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5855 (ptm-80) REVERT: P 4 MET cc_start: 0.8727 (mmm) cc_final: 0.8370 (mmm) REVERT: P 54 TYR cc_start: 0.6997 (t80) cc_final: 0.6739 (t80) REVERT: P 80 ILE cc_start: 0.5807 (mt) cc_final: 0.5497 (mm) REVERT: P 108 LYS cc_start: 0.7456 (mttt) cc_final: 0.7172 (tptt) REVERT: F 76 GLN cc_start: 0.8725 (tp40) cc_final: 0.8368 (tm-30) REVERT: F 82 ASN cc_start: 0.8658 (m110) cc_final: 0.8365 (m-40) REVERT: H 118 GLN cc_start: 0.8736 (tp40) cc_final: 0.8503 (tp-100) REVERT: H 149 GLN cc_start: 0.8357 (tp40) cc_final: 0.8128 (tp-100) REVERT: H 150 LEU cc_start: 0.9037 (mm) cc_final: 0.8623 (mp) REVERT: H 182 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8014 (mtmt) REVERT: H 183 MET cc_start: 0.8777 (ttm) cc_final: 0.8331 (ttm) REVERT: J 30 ASN cc_start: 0.8213 (m-40) cc_final: 0.7990 (t0) REVERT: J 197 TYR cc_start: 0.8593 (t80) cc_final: 0.8364 (t80) REVERT: J 199 ASN cc_start: 0.9073 (t0) cc_final: 0.8362 (t0) REVERT: J 231 GLU cc_start: 0.8574 (pt0) cc_final: 0.8290 (pt0) REVERT: L 30 ASN cc_start: 0.7372 (m-40) cc_final: 0.7078 (p0) REVERT: L 76 LYS cc_start: 0.8680 (mttt) cc_final: 0.8265 (mtpp) REVERT: L 84 ASP cc_start: 0.8158 (t70) cc_final: 0.7856 (t0) REVERT: N 52 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8976 (mm) REVERT: N 62 GLU cc_start: 0.8647 (mp0) cc_final: 0.8302 (mp0) REVERT: Q 108 TYR cc_start: 0.9130 (m-80) cc_final: 0.8785 (m-80) REVERT: R 3 GLN cc_start: 0.7974 (pt0) cc_final: 0.7392 (pm20) REVERT: R 22 CYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7303 (p) REVERT: R 95 TYR cc_start: 0.6409 (m-80) cc_final: 0.6057 (m-80) REVERT: S 4 MET cc_start: 0.8659 (mmm) cc_final: 0.8395 (mmm) REVERT: S 24 LYS cc_start: 0.6426 (ttmm) cc_final: 0.6081 (tppt) REVERT: S 54 TYR cc_start: 0.6929 (t80) cc_final: 0.6667 (t80) REVERT: S 80 ILE cc_start: 0.5716 (mt) cc_final: 0.5375 (mm) outliers start: 98 outliers final: 70 residues processed: 699 average time/residue: 0.3452 time to fit residues: 366.9475 Evaluate side-chains 711 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 636 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 92 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 75 SER Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain 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 208 ASN Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 CYS 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 104 LEU Chi-restraints excluded: chain M residue 105 CYS Chi-restraints excluded: chain M residue 136 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 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 185 ASP Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER 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 52 ILE Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 225 THR Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 38 VAL 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 169 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 163 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 215 optimal weight: 0.4980 chunk 249 optimal weight: 4.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- 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 ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 245 HIS H 227 ASN J 109 HIS J 152 GLN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23234 Z= 0.152 Angle : 0.542 7.698 31746 Z= 0.270 Chirality : 0.043 0.176 3580 Planarity : 0.004 0.049 4038 Dihedral : 4.178 22.938 3096 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.90 % Allowed : 20.70 % Favored : 75.40 % 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: -1.10 (0.15), residues: 2826 helix: -2.27 (0.42), residues: 124 sheet: -0.38 (0.17), residues: 824 loop : -0.78 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 203 HIS 0.004 0.001 HIS F 245 PHE 0.028 0.001 PHE N 28 TYR 0.025 0.001 TYR F 106 ARG 0.008 0.000 ARG F 254 *********************** 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 732 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 635 time to evaluate : 2.574 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: D 76 GLN cc_start: 0.8676 (tp40) cc_final: 0.8335 (tm-30) REVERT: D 82 ASN cc_start: 0.8712 (m110) cc_final: 0.8352 (m-40) REVERT: E 119 LEU cc_start: 0.8585 (tp) cc_final: 0.8288 (tp) REVERT: E 128 TYR cc_start: 0.9237 (m-80) cc_final: 0.8985 (m-10) REVERT: E 149 GLN cc_start: 0.8523 (tp40) cc_final: 0.8284 (tp-100) REVERT: E 162 LYS cc_start: 0.8929 (mttm) cc_final: 0.8655 (mtpp) REVERT: E 183 MET cc_start: 0.8849 (ttm) cc_final: 0.8437 (ttm) REVERT: E 276 ASN cc_start: 0.8655 (p0) cc_final: 0.8388 (p0) REVERT: E 278 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8536 (m-40) REVERT: E 280 LYS cc_start: 0.8495 (tttt) cc_final: 0.8082 (tppt) REVERT: G 103 ARG cc_start: 0.8432 (ptm160) cc_final: 0.8135 (ptm160) REVERT: G 127 LEU cc_start: 0.8654 (tp) cc_final: 0.8392 (tp) REVERT: G 199 ASN cc_start: 0.9078 (t0) cc_final: 0.8599 (t0) REVERT: G 231 GLU cc_start: 0.8667 (pt0) cc_final: 0.8357 (pt0) REVERT: I 30 ASN cc_start: 0.7320 (m-40) cc_final: 0.7046 (p0) REVERT: I 76 LYS cc_start: 0.8630 (mttt) cc_final: 0.8305 (mtpp) REVERT: I 84 ASP cc_start: 0.8074 (t70) cc_final: 0.7675 (t0) REVERT: I 152 GLN cc_start: 0.8664 (mm110) cc_final: 0.8450 (mm-40) REVERT: K 62 GLU cc_start: 0.8716 (mp0) cc_final: 0.8278 (mp0) REVERT: K 92 ARG cc_start: 0.8853 (ptp-110) cc_final: 0.8244 (mtp85) REVERT: K 226 MET cc_start: 0.8178 (mtt) cc_final: 0.7853 (mtp) REVERT: M 48 ARG cc_start: 0.8629 (mtt90) cc_final: 0.8224 (mtt-85) REVERT: O 3 GLN cc_start: 0.7969 (pt0) cc_final: 0.7382 (pm20) REVERT: O 63 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8013 (mtmm) REVERT: O 95 TYR cc_start: 0.6526 (m-80) cc_final: 0.6276 (m-80) REVERT: O 98 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5869 (ptm-80) REVERT: P 4 MET cc_start: 0.8679 (mmm) cc_final: 0.8233 (mmm) REVERT: P 54 TYR cc_start: 0.7029 (t80) cc_final: 0.6786 (t80) REVERT: P 80 ILE cc_start: 0.5657 (mt) cc_final: 0.5381 (mm) REVERT: P 108 LYS cc_start: 0.7454 (mttt) cc_final: 0.7168 (tptt) REVERT: F 76 GLN cc_start: 0.8710 (tp40) cc_final: 0.8429 (tm-30) REVERT: F 82 ASN cc_start: 0.8672 (m110) cc_final: 0.8412 (m-40) REVERT: H 118 GLN cc_start: 0.8780 (tp40) cc_final: 0.8525 (tp-100) REVERT: H 150 LEU cc_start: 0.9044 (mm) cc_final: 0.8806 (mp) REVERT: H 183 MET cc_start: 0.8757 (ttm) cc_final: 0.8299 (ttm) REVERT: H 278 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: J 30 ASN cc_start: 0.8203 (m-40) cc_final: 0.7987 (t0) REVERT: J 199 ASN cc_start: 0.9075 (t0) cc_final: 0.8389 (t0) REVERT: J 231 GLU cc_start: 0.8568 (pt0) cc_final: 0.8254 (pt0) REVERT: L 30 ASN cc_start: 0.7370 (m-40) cc_final: 0.7090 (p0) REVERT: L 76 LYS cc_start: 0.8626 (mttt) cc_final: 0.8278 (mtpp) REVERT: L 84 ASP cc_start: 0.8148 (t70) cc_final: 0.7865 (t0) REVERT: L 100 TYR cc_start: 0.6669 (t80) cc_final: 0.5847 (t80) REVERT: N 52 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8955 (mm) REVERT: N 62 GLU cc_start: 0.8673 (mp0) cc_final: 0.8334 (mp0) REVERT: N 92 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.8266 (mtp85) REVERT: Q 108 TYR cc_start: 0.9123 (m-80) cc_final: 0.8765 (m-80) REVERT: R 22 CYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7369 (p) REVERT: R 63 LYS cc_start: 0.8276 (mtmm) cc_final: 0.8024 (mtmm) REVERT: R 95 TYR cc_start: 0.6232 (m-80) cc_final: 0.6001 (m-80) REVERT: S 4 MET cc_start: 0.8670 (mmm) cc_final: 0.8436 (mmm) REVERT: S 24 LYS cc_start: 0.6361 (ttmm) cc_final: 0.6039 (tppt) REVERT: S 80 ILE cc_start: 0.5661 (mt) cc_final: 0.5340 (mm) outliers start: 97 outliers final: 73 residues processed: 689 average time/residue: 0.3482 time to fit residues: 364.5683 Evaluate side-chains 705 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 627 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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 185 ASP 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 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 190 CYS 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 231 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 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 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 42 GLN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 HIS 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 164 THR Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 52 ILE 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 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 38 VAL 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 262 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** K 154 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 227 ASN J 109 HIS J 152 GLN N 67 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 HIS ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23234 Z= 0.319 Angle : 0.627 8.984 31746 Z= 0.316 Chirality : 0.046 0.176 3580 Planarity : 0.005 0.052 4038 Dihedral : 4.639 25.110 3096 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.70 % Allowed : 21.26 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 2826 helix: -2.07 (0.47), residues: 112 sheet: -0.52 (0.17), residues: 842 loop : -0.91 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 104 HIS 0.004 0.001 HIS I 109 PHE 0.025 0.002 PHE R 27 TYR 0.035 0.002 TYR S 54 ARG 0.011 0.001 ARG F 254 *********************** 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 690 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 598 time to evaluate : 2.665 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: 0.8359 (tm-30) REVERT: D 82 ASN cc_start: 0.8744 (m110) cc_final: 0.8473 (m-40) REVERT: D 95 MET cc_start: 0.7750 (ttp) cc_final: 0.7473 (tmm) REVERT: E 149 GLN cc_start: 0.8497 (tp40) cc_final: 0.8285 (tp-100) REVERT: E 162 LYS cc_start: 0.9038 (mttm) cc_final: 0.8720 (mtpp) REVERT: E 183 MET cc_start: 0.8798 (ttm) cc_final: 0.8377 (ttm) REVERT: E 280 LYS cc_start: 0.8620 (tttt) cc_final: 0.8131 (tppt) REVERT: G 127 LEU cc_start: 0.8719 (tp) cc_final: 0.8512 (tp) REVERT: G 199 ASN cc_start: 0.9028 (t0) cc_final: 0.8561 (t0) REVERT: G 231 GLU cc_start: 0.8657 (pt0) cc_final: 0.8381 (pt0) REVERT: I 30 ASN cc_start: 0.7547 (m-40) cc_final: 0.7022 (p0) REVERT: I 76 LYS cc_start: 0.8814 (mttt) cc_final: 0.8496 (mtpp) REVERT: I 84 ASP cc_start: 0.8346 (t70) cc_final: 0.7924 (t0) REVERT: I 241 MET cc_start: 0.7468 (mmm) cc_final: 0.6948 (mtp) REVERT: K 62 GLU cc_start: 0.8792 (mp0) cc_final: 0.8346 (mp0) REVERT: K 92 ARG cc_start: 0.8898 (ptp-110) cc_final: 0.8366 (mtp85) REVERT: K 226 MET cc_start: 0.8216 (mtt) cc_final: 0.7907 (mtp) REVERT: O 63 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8107 (mtmm) REVERT: O 73 ASP cc_start: 0.6201 (t0) cc_final: 0.5604 (t0) REVERT: P 4 MET cc_start: 0.8727 (mmm) cc_final: 0.8450 (mmm) REVERT: P 54 TYR cc_start: 0.7002 (t80) cc_final: 0.6737 (t80) REVERT: P 80 ILE cc_start: 0.5725 (mt) cc_final: 0.5432 (mm) REVERT: F 76 GLN cc_start: 0.8687 (tp40) cc_final: 0.8387 (tm-30) REVERT: F 82 ASN cc_start: 0.8665 (m110) cc_final: 0.8463 (m-40) REVERT: H 118 GLN cc_start: 0.8870 (tp40) cc_final: 0.8615 (tp-100) REVERT: H 183 MET cc_start: 0.8726 (ttm) cc_final: 0.8290 (ttm) REVERT: H 280 LYS cc_start: 0.8537 (tttt) cc_final: 0.8076 (tppt) REVERT: J 30 ASN cc_start: 0.8406 (m-40) cc_final: 0.8107 (t0) REVERT: J 40 GLU cc_start: 0.8441 (tp30) cc_final: 0.8240 (tp30) REVERT: J 199 ASN cc_start: 0.9108 (t0) cc_final: 0.8787 (t0) REVERT: J 231 GLU cc_start: 0.8571 (pt0) cc_final: 0.8321 (pt0) REVERT: L 30 ASN cc_start: 0.7575 (m-40) cc_final: 0.7079 (p0) REVERT: L 76 LYS cc_start: 0.8837 (mttt) cc_final: 0.8502 (mtpp) REVERT: L 84 ASP cc_start: 0.8334 (t70) cc_final: 0.7964 (t0) REVERT: L 241 MET cc_start: 0.7504 (mmm) cc_final: 0.7010 (mtp) REVERT: N 50 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: N 52 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9062 (mm) REVERT: N 62 GLU cc_start: 0.8736 (mp0) cc_final: 0.8390 (mp0) REVERT: Q 48 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7946 (mtt-85) REVERT: R 22 CYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7439 (p) REVERT: R 73 ASP cc_start: 0.6164 (t0) cc_final: 0.5567 (t0) REVERT: S 54 TYR cc_start: 0.6856 (t80) cc_final: 0.6528 (t80) REVERT: S 80 ILE cc_start: 0.5736 (mt) cc_final: 0.5400 (mm) outliers start: 92 outliers final: 66 residues processed: 654 average time/residue: 0.3702 time to fit residues: 369.1085 Evaluate side-chains 655 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 586 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 185 ASP 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 146 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 190 CYS Chi-restraints excluded: chain G residue 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 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 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 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 255 ILE Chi-restraints excluded: chain F residue 257 HIS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 143 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 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 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 47 CYS Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 TYR Chi-restraints excluded: chain S residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 chunk 127 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 260 optimal weight: 0.0970 chunk 225 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN K 97 GLN P 43 GLN P 105 GLN ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN H 227 ASN H 276 ASN J 109 HIS J 152 GLN L 155 GLN N 67 GLN N 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23234 Z= 0.159 Angle : 0.568 8.805 31746 Z= 0.283 Chirality : 0.044 0.159 3580 Planarity : 0.004 0.048 4038 Dihedral : 4.343 23.260 3096 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.22 % Allowed : 21.58 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2826 helix: -1.98 (0.47), residues: 114 sheet: -0.45 (0.18), residues: 814 loop : -0.76 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 203 HIS 0.003 0.001 HIS I 109 PHE 0.029 0.001 PHE N 28 TYR 0.031 0.001 TYR S 54 ARG 0.008 0.001 ARG F 254 ********************** 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 703 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 623 time to evaluate : 2.477 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: D 76 GLN cc_start: 0.8629 (tp40) cc_final: 0.8408 (tm-30) REVERT: D 82 ASN cc_start: 0.8733 (m110) cc_final: 0.8491 (m-40) REVERT: D 95 MET cc_start: 0.7747 (ttp) cc_final: 0.7494 (tmm) REVERT: D 153 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6872 (m-10) REVERT: E 119 LEU cc_start: 0.8596 (tp) cc_final: 0.8360 (tp) REVERT: E 128 TYR cc_start: 0.9155 (m-80) cc_final: 0.8917 (m-10) REVERT: E 146 LEU cc_start: 0.7711 (mp) cc_final: 0.7321 (mt) REVERT: E 149 GLN cc_start: 0.8415 (tp40) cc_final: 0.8059 (tp-100) REVERT: E 162 LYS cc_start: 0.9036 (mttm) cc_final: 0.8712 (mtpp) REVERT: E 183 MET cc_start: 0.8823 (ttm) cc_final: 0.8442 (ttm) REVERT: E 280 LYS cc_start: 0.8532 (tttt) cc_final: 0.8044 (tppt) REVERT: G 64 PHE cc_start: 0.9200 (m-80) cc_final: 0.8840 (m-80) REVERT: G 127 LEU cc_start: 0.8638 (tp) cc_final: 0.8361 (tp) REVERT: G 199 ASN cc_start: 0.9027 (t0) cc_final: 0.8582 (t0) REVERT: G 231 GLU cc_start: 0.8677 (pt0) cc_final: 0.8337 (pt0) REVERT: I 30 ASN cc_start: 0.7484 (m-40) cc_final: 0.7113 (p0) REVERT: I 76 LYS cc_start: 0.8626 (mttt) cc_final: 0.8298 (mtpp) REVERT: I 84 ASP cc_start: 0.8169 (t70) cc_final: 0.7795 (t0) REVERT: I 241 MET cc_start: 0.7369 (mmm) cc_final: 0.6869 (mtp) REVERT: K 92 ARG cc_start: 0.8824 (ptp-110) cc_final: 0.8139 (mtp85) REVERT: K 226 MET cc_start: 0.8234 (mtt) cc_final: 0.7901 (mtp) REVERT: K 231 ASP cc_start: 0.8873 (t0) cc_final: 0.8633 (t0) REVERT: O 73 ASP cc_start: 0.6074 (t0) cc_final: 0.5491 (t0) REVERT: P 80 ILE cc_start: 0.5592 (mt) cc_final: 0.5328 (mm) REVERT: H 118 GLN cc_start: 0.8831 (tp40) cc_final: 0.8559 (tp-100) REVERT: H 183 MET cc_start: 0.8677 (ttm) cc_final: 0.8233 (ttm) REVERT: H 280 LYS cc_start: 0.8518 (tttt) cc_final: 0.8003 (tppt) REVERT: J 30 ASN cc_start: 0.8204 (m-40) cc_final: 0.7959 (t0) REVERT: J 199 ASN cc_start: 0.9040 (t0) cc_final: 0.8708 (t0) REVERT: J 231 GLU cc_start: 0.8574 (pt0) cc_final: 0.8206 (pt0) REVERT: L 30 ASN cc_start: 0.7512 (m-40) cc_final: 0.7144 (p0) REVERT: L 76 LYS cc_start: 0.8600 (mttt) cc_final: 0.8263 (mtpp) REVERT: L 84 ASP cc_start: 0.8187 (t70) cc_final: 0.7867 (t0) REVERT: L 241 MET cc_start: 0.7403 (mmm) cc_final: 0.6946 (mtp) REVERT: N 50 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: N 52 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (mm) REVERT: N 62 GLU cc_start: 0.8729 (mp0) cc_final: 0.8388 (mp0) REVERT: N 92 ARG cc_start: 0.8824 (ptp-110) cc_final: 0.8166 (mtp85) REVERT: R 3 GLN cc_start: 0.7997 (pt0) cc_final: 0.7467 (pm20) REVERT: R 22 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7432 (p) REVERT: R 73 ASP cc_start: 0.6211 (t0) cc_final: 0.5611 (t0) outliers start: 80 outliers final: 58 residues processed: 666 average time/residue: 0.3484 time to fit residues: 350.4950 Evaluate side-chains 661 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 599 time to evaluate : 2.894 ------------------------------------------------------------------------------- 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 153 TYR 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 164 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain K residue 50 GLU Chi-restraints excluded: chain M residue 55 VAL 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 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 156 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 143 ASN Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 276 ASN 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 115 SER Chi-restraints excluded: chain N residue 47 CYS Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 67 GLN Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 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 S residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN G 152 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN H 276 ASN J 109 HIS J 152 GLN ** N 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097260 restraints weight = 37823.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100962 restraints weight = 21583.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103352 restraints weight = 15199.797| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23234 Z= 0.381 Angle : 0.666 9.542 31746 Z= 0.337 Chirality : 0.047 0.182 3580 Planarity : 0.005 0.071 4038 Dihedral : 4.761 26.533 3096 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.22 % Allowed : 21.74 % Favored : 75.04 % 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: -1.35 (0.15), residues: 2826 helix: -1.85 (0.51), residues: 104 sheet: -0.62 (0.17), residues: 820 loop : -0.98 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 104 HIS 0.005 0.001 HIS I 109 PHE 0.024 0.002 PHE R 27 TYR 0.035 0.002 TYR P 54 ARG 0.015 0.001 ARG N 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6541.21 seconds wall clock time: 115 minutes 49.52 seconds (6949.52 seconds total)