Starting phenix.real_space_refine on Wed Mar 4 01:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykp_10829/03_2026/6ykp_10829.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.119 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 70 5.16 5 C 6592 2.51 5 N 1649 2.21 5 O 1879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10190 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Classifications: {'peptide': 25} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 22} Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 210 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10190 At special positions: 0 Unit cell: (92.352, 97.344, 112.32, 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 70 16.00 O 1879 8.00 N 1649 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 473.5 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.505A pdb=" N ASP A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.663A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.901A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.718A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.891A pdb=" N GLN A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.651A pdb=" N LEU A 96 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.558A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.528A pdb=" N GLU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 137 through 171 removed outlier: 3.507A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.722A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 184 through 199 removed outlier: 4.265A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.516A pdb=" N LYS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.537A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'B' and resid 2 through 22 removed outlier: 3.523A pdb=" N MET B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 22 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.774A pdb=" N VAL B 30 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.832A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.720A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.571A pdb=" N ALA B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.713A pdb=" N GLU B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.544A pdb=" N ASN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.782A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 171 removed outlier: 3.573A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.582A pdb=" N GLY B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.556A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 3.553A pdb=" N ALA B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'C' and resid 2 through 22 removed outlier: 3.952A pdb=" N MET C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.562A pdb=" N HIS C 29 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 30 " --> pdb=" O PRO C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 30' Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.508A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.587A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.513A pdb=" N ALA C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.589A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.502A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.614A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 170 removed outlier: 3.626A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Proline residue: C 154 - end of helix removed outlier: 3.649A pdb=" N LEU C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.680A pdb=" N ALA C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.802A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.975A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.549A pdb=" N ASP D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.738A pdb=" N VAL D 30 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.702A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.658A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 removed outlier: 3.709A pdb=" N GLN D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 removed outlier: 3.604A pdb=" N LEU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.529A pdb=" N ASP D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.500A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 142 through 171 removed outlier: 4.104A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.642A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 167 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.514A pdb=" N MET D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 198 removed outlier: 3.873A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 211 Processing helix chain 'D' and resid 214 through 229 Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.652A pdb=" N ALA D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.591A pdb=" N LEU E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.687A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.730A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 91 removed outlier: 3.803A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 100 removed outlier: 3.714A pdb=" N GLU E 97 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.586A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 171 removed outlier: 3.998A pdb=" N TRP E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS E 153 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.784A pdb=" N ILE E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 167 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 185 through 197 removed outlier: 3.748A pdb=" N THR E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.932A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.634A pdb=" N ALA E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 23 through 39 removed outlier: 3.568A pdb=" N LEU F 27 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 40 removed outlier: 4.735A pdb=" N LEU G 26 " --> pdb=" O ASP G 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU G 27 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1776 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: 1.14 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2282 1.33 - 1.45: 2111 1.45 - 1.57: 5853 1.57 - 1.69: 1 1.69 - 1.81: 125 Bond restraints: 10372 Sorted by residual: bond pdb=" CB PRO C 154 " pdb=" CG PRO C 154 " ideal model delta sigma weight residual 1.492 1.318 0.174 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CB THR D 5 " pdb=" CG2 THR D 5 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.76e+00 bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.364 0.128 5.00e-02 4.00e+02 6.57e+00 bond pdb=" CB PRO D 202 " pdb=" CG PRO D 202 " ideal model delta sigma weight residual 1.492 1.367 0.125 5.00e-02 4.00e+02 6.24e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 13791 3.83 - 7.67: 192 7.67 - 11.50: 22 11.50 - 15.34: 5 15.34 - 19.17: 4 Bond angle restraints: 14014 Sorted by residual: angle pdb=" C ASP F 22 " pdb=" N PHE F 23 " pdb=" CA PHE F 23 " ideal model delta sigma weight residual 121.70 140.87 -19.17 1.80e+00 3.09e-01 1.13e+02 angle pdb=" C VAL F 18 " pdb=" N PRO F 19 " pdb=" CA PRO F 19 " ideal model delta sigma weight residual 120.96 131.71 -10.75 1.41e+00 5.03e-01 5.81e+01 angle pdb=" CB LEU C 158 " pdb=" CG LEU C 158 " pdb=" CD2 LEU C 158 " ideal model delta sigma weight residual 110.70 93.91 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" CA LEU E 171 " pdb=" CB LEU E 171 " pdb=" CG LEU E 171 " ideal model delta sigma weight residual 116.30 134.27 -17.97 3.50e+00 8.16e-02 2.64e+01 angle pdb=" N TYR F 20 " pdb=" CA TYR F 20 " pdb=" C TYR F 20 " ideal model delta sigma weight residual 110.80 100.31 10.49 2.13e+00 2.20e-01 2.43e+01 ... (remaining 14009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 6070 23.66 - 47.32: 128 47.32 - 70.99: 16 70.99 - 94.65: 2 94.65 - 118.31: 2 Dihedral angle restraints: 6218 sinusoidal: 2425 harmonic: 3793 Sorted by residual: dihedral pdb=" CA ALA F 21 " pdb=" C ALA F 21 " pdb=" N ASP F 22 " pdb=" CA ASP F 22 " ideal model delta harmonic sigma weight residual 180.00 61.69 118.31 0 5.00e+00 4.00e-02 5.60e+02 dihedral pdb=" CA VAL F 18 " pdb=" C VAL F 18 " pdb=" N PRO F 19 " pdb=" CA PRO F 19 " ideal model delta harmonic sigma weight residual 180.00 74.94 105.06 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" CA ASP F 22 " pdb=" C ASP F 22 " pdb=" N PHE F 23 " pdb=" CA PHE F 23 " ideal model delta harmonic sigma weight residual 0.00 -30.48 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 6215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1420 0.099 - 0.197: 198 0.197 - 0.296: 19 0.296 - 0.395: 2 0.395 - 0.493: 1 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CB VAL F 18 " pdb=" CA VAL F 18 " pdb=" CG1 VAL F 18 " pdb=" CG2 VAL F 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL G 18 " pdb=" CA VAL G 18 " pdb=" CG1 VAL G 18 " pdb=" CG2 VAL G 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1637 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 149 " 0.030 2.00e-02 2.50e+03 3.65e-02 2.34e+01 pdb=" CG PHE E 149 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE E 149 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE E 149 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE E 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 149 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE E 149 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.026 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE C 149 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " -0.026 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 149 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " -0.001 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3483 2.86 - 3.37: 9895 3.37 - 3.88: 16736 3.88 - 4.39: 21342 4.39 - 4.90: 34121 Nonbonded interactions: 85577 Sorted by model distance: nonbonded pdb=" OH TYR B 60 " pdb=" OH TYR B 145 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR E 189 " pdb=" OD1 ASP G 22 " model vdw 2.360 3.040 nonbonded pdb=" OH TYR E 60 " pdb=" OH TYR E 145 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR C 60 " pdb=" OH TYR C 145 " model vdw 2.382 3.040 nonbonded pdb=" NH1 ARG B 77 " pdb=" OE1 GLN B 80 " model vdw 2.393 3.120 ... (remaining 85572 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 15 through 39) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.014 0.174 10372 Z= 0.584 Angle : 1.228 19.173 14014 Z= 0.626 Chirality : 0.072 0.493 1640 Planarity : 0.009 0.084 1763 Dihedral : 10.753 118.312 3766 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 1.02 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.56 (0.13), residues: 1312 helix: -4.62 (0.07), residues: 1051 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 251 TYR 0.041 0.005 TYR F 20 PHE 0.081 0.005 PHE E 149 TRP 0.026 0.004 TRP F 16 HIS 0.017 0.004 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.01433 (10372) covalent geometry : angle 1.22835 (14014) hydrogen bonds : bond 0.29371 ( 605) hydrogen bonds : angle 11.88138 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.365 Fit side-chains REVERT: A 64 LYS cc_start: 0.7573 (mttm) cc_final: 0.7317 (mtpm) REVERT: A 68 LYS cc_start: 0.8521 (tttp) cc_final: 0.7818 (mptt) REVERT: A 116 VAL cc_start: 0.8527 (t) cc_final: 0.8275 (m) REVERT: A 122 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7365 (mm-30) REVERT: A 129 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7101 (pt0) REVERT: B 83 GLU cc_start: 0.7393 (tt0) cc_final: 0.7050 (tt0) REVERT: B 94 LEU cc_start: 0.8584 (pp) cc_final: 0.7941 (tm) REVERT: B 117 ASP cc_start: 0.8104 (m-30) cc_final: 0.7895 (m-30) REVERT: B 138 HIS cc_start: 0.7339 (t70) cc_final: 0.6834 (t-170) REVERT: B 140 LYS cc_start: 0.8104 (ttmp) cc_final: 0.7763 (ttpp) REVERT: C 35 SER cc_start: 0.8835 (m) cc_final: 0.8503 (p) REVERT: C 94 LEU cc_start: 0.8764 (pp) cc_final: 0.8443 (pt) REVERT: C 104 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7541 (mp0) REVERT: C 106 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7454 (mp0) REVERT: C 129 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6955 (mm-30) REVERT: C 197 TYR cc_start: 0.8861 (m-80) cc_final: 0.8653 (m-80) REVERT: C 216 LYS cc_start: 0.7910 (tttt) cc_final: 0.7192 (mttp) REVERT: D 57 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7735 (mttt) REVERT: D 61 LYS cc_start: 0.8003 (mttt) cc_final: 0.7596 (mtmm) REVERT: D 64 LYS cc_start: 0.7548 (mttm) cc_final: 0.6961 (mmmt) REVERT: D 83 GLU cc_start: 0.7511 (tt0) cc_final: 0.7027 (mt-10) REVERT: D 102 GLU cc_start: 0.8000 (pp20) cc_final: 0.7704 (pp20) REVERT: D 140 LYS cc_start: 0.8316 (ttmp) cc_final: 0.7702 (ttpp) REVERT: D 226 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7829 (ttpt) REVERT: D 230 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6846 (mt-10) REVERT: E 97 GLU cc_start: 0.8300 (tt0) cc_final: 0.8064 (tt0) REVERT: E 123 GLU cc_start: 0.7865 (tp30) cc_final: 0.7633 (tm-30) REVERT: E 212 MET cc_start: 0.7990 (mmm) cc_final: 0.7773 (mmp) REVERT: E 230 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7047 (pt0) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.7215 time to fit residues: 190.3991 Evaluate side-chains 180 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 52 HIS B 125 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 254 GLN E 125 HIS E 210 ASN ** E 243 ASN ** 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 = 0.3670 r_free = 0.3670 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110593 restraints weight = 11467.121| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.23 r_work: 0.3159 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10372 Z= 0.131 Angle : 0.634 13.507 14014 Z= 0.326 Chirality : 0.043 0.261 1640 Planarity : 0.006 0.081 1763 Dihedral : 5.917 53.488 1371 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 2.50 % Allowed : 9.99 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.19), residues: 1312 helix: -2.83 (0.12), residues: 1068 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 251 TYR 0.011 0.001 TYR C 197 PHE 0.020 0.002 PHE B 149 TRP 0.008 0.001 TRP A 203 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00301 (10372) covalent geometry : angle 0.63358 (14014) hydrogen bonds : bond 0.03685 ( 605) hydrogen bonds : angle 5.28378 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.247 Fit side-chains REVERT: A 57 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7785 (tptt) REVERT: A 64 LYS cc_start: 0.7889 (mttm) cc_final: 0.7550 (ptmm) REVERT: A 68 LYS cc_start: 0.8672 (tttp) cc_final: 0.7801 (mptt) REVERT: A 113 MET cc_start: 0.8182 (mtm) cc_final: 0.7938 (mtp) REVERT: A 122 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7636 (mm-30) REVERT: A 126 GLU cc_start: 0.8721 (tp30) cc_final: 0.8416 (mt-10) REVERT: A 129 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7340 (pt0) REVERT: B 83 GLU cc_start: 0.7619 (tt0) cc_final: 0.7295 (pt0) REVERT: B 94 LEU cc_start: 0.8442 (pp) cc_final: 0.7866 (tm) REVERT: B 138 HIS cc_start: 0.7533 (t70) cc_final: 0.7309 (t70) REVERT: C 1 MET cc_start: 0.6277 (tpp) cc_final: 0.5573 (tmt) REVERT: C 3 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7950 (mp) REVERT: C 29 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: C 35 SER cc_start: 0.8794 (m) cc_final: 0.8569 (p) REVERT: C 104 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7688 (mm-30) REVERT: C 106 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 129 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7395 (tp30) REVERT: D 28 LEU cc_start: 0.8077 (mp) cc_final: 0.7865 (mm) REVERT: D 61 LYS cc_start: 0.8341 (mttt) cc_final: 0.7625 (mptt) REVERT: D 64 LYS cc_start: 0.7913 (mttm) cc_final: 0.7214 (mmtt) REVERT: D 83 GLU cc_start: 0.7936 (tt0) cc_final: 0.7171 (mt-10) REVERT: D 102 GLU cc_start: 0.8102 (pp20) cc_final: 0.7828 (pp20) REVERT: D 126 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 140 LYS cc_start: 0.8538 (ttmp) cc_final: 0.7865 (ttpp) REVERT: D 170 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8242 (ttmt) REVERT: E 97 GLU cc_start: 0.8602 (tt0) cc_final: 0.8377 (tt0) REVERT: E 104 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: E 113 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7245 (tpp) REVERT: E 123 GLU cc_start: 0.8019 (tp30) cc_final: 0.7619 (tm-30) REVERT: E 178 MET cc_start: 0.7376 (ttp) cc_final: 0.7084 (tmm) REVERT: E 212 MET cc_start: 0.8195 (mmm) cc_final: 0.7700 (mmp) REVERT: E 230 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7183 (pt0) REVERT: E 235 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7422 (tpp80) outliers start: 27 outliers final: 5 residues processed: 216 average time/residue: 0.6332 time to fit residues: 145.4445 Evaluate side-chains 178 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 243 ASN B 110 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS E 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110471 restraints weight = 11417.478| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.22 r_work: 0.3156 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10372 Z= 0.124 Angle : 0.589 13.701 14014 Z= 0.294 Chirality : 0.042 0.264 1640 Planarity : 0.005 0.069 1763 Dihedral : 5.332 47.913 1371 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 3.15 % Allowed : 13.23 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1312 helix: -1.64 (0.14), residues: 1076 sheet: None (None), residues: 0 loop : -0.20 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 251 TYR 0.009 0.001 TYR E 145 PHE 0.018 0.002 PHE D 121 TRP 0.019 0.001 TRP F 16 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00290 (10372) covalent geometry : angle 0.58904 (14014) hydrogen bonds : bond 0.03144 ( 605) hydrogen bonds : angle 4.55222 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.397 Fit side-chains REVERT: A 57 LYS cc_start: 0.8520 (ttmm) cc_final: 0.7776 (tptt) REVERT: A 64 LYS cc_start: 0.7898 (mttm) cc_final: 0.7643 (ptmm) REVERT: A 68 LYS cc_start: 0.8676 (tttp) cc_final: 0.7678 (mptt) REVERT: A 113 MET cc_start: 0.8170 (mtm) cc_final: 0.7795 (mtp) REVERT: A 117 ASP cc_start: 0.7903 (m-30) cc_final: 0.7628 (m-30) REVERT: A 129 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7446 (pt0) REVERT: A 151 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7705 (pt0) REVERT: B 83 GLU cc_start: 0.7622 (tt0) cc_final: 0.7289 (pt0) REVERT: B 94 LEU cc_start: 0.8448 (pp) cc_final: 0.7995 (tm) REVERT: B 110 ASN cc_start: 0.8231 (m110) cc_final: 0.7620 (t0) REVERT: B 126 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: C 1 MET cc_start: 0.6273 (tpp) cc_final: 0.5577 (tmt) REVERT: C 3 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7877 (mp) REVERT: C 29 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7246 (m-70) REVERT: C 94 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 104 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7697 (mm-30) REVERT: C 106 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7562 (mp0) REVERT: C 112 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: D 28 LEU cc_start: 0.8122 (mp) cc_final: 0.7909 (mm) REVERT: D 29 HIS cc_start: 0.8114 (m170) cc_final: 0.7911 (m-70) REVERT: D 57 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7977 (ttmm) REVERT: D 61 LYS cc_start: 0.8350 (mttt) cc_final: 0.7637 (mptt) REVERT: D 64 LYS cc_start: 0.7844 (mttm) cc_final: 0.7143 (mmtt) REVERT: D 83 GLU cc_start: 0.7909 (tt0) cc_final: 0.7091 (mt-10) REVERT: D 102 GLU cc_start: 0.8006 (pp20) cc_final: 0.7759 (pp20) REVERT: D 113 MET cc_start: 0.8482 (mmm) cc_final: 0.8212 (mmm) REVERT: D 126 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 129 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7533 (pt0) REVERT: D 140 LYS cc_start: 0.8448 (ttmp) cc_final: 0.7776 (ttpp) REVERT: D 170 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8208 (ttmt) REVERT: D 254 GLN cc_start: 0.8470 (tt0) cc_final: 0.7818 (tt0) REVERT: E 94 LEU cc_start: 0.8782 (pt) cc_final: 0.8323 (mm) REVERT: E 112 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7785 (mmt) REVERT: E 113 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7165 (tpp) REVERT: E 123 GLU cc_start: 0.8091 (tp30) cc_final: 0.7787 (tt0) REVERT: E 178 MET cc_start: 0.7344 (ttp) cc_final: 0.7123 (tmm) REVERT: E 212 MET cc_start: 0.8196 (mmm) cc_final: 0.7874 (mmp) REVERT: E 230 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7060 (pt0) REVERT: E 235 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7511 (tpp80) outliers start: 34 outliers final: 8 residues processed: 189 average time/residue: 0.6279 time to fit residues: 126.3332 Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN E 138 HIS E 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107043 restraints weight = 11548.514| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.23 r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10372 Z= 0.158 Angle : 0.598 13.659 14014 Z= 0.298 Chirality : 0.044 0.284 1640 Planarity : 0.004 0.079 1763 Dihedral : 5.123 44.778 1371 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 3.42 % Allowed : 14.25 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1312 helix: -1.03 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : 0.07 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 99 TYR 0.011 0.002 TYR E 145 PHE 0.019 0.002 PHE C 149 TRP 0.007 0.001 TRP D 146 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00383 (10372) covalent geometry : angle 0.59831 (14014) hydrogen bonds : bond 0.03199 ( 605) hydrogen bonds : angle 4.33394 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.370 Fit side-chains REVERT: A 57 LYS cc_start: 0.8526 (ttmm) cc_final: 0.7795 (tptt) REVERT: A 64 LYS cc_start: 0.7835 (mttm) cc_final: 0.7603 (ptmm) REVERT: A 68 LYS cc_start: 0.8677 (tttp) cc_final: 0.7764 (mptt) REVERT: A 113 MET cc_start: 0.8103 (mtm) cc_final: 0.7899 (mtp) REVERT: A 126 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: A 129 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7453 (tt0) REVERT: A 151 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7690 (pt0) REVERT: B 83 GLU cc_start: 0.7657 (tt0) cc_final: 0.7319 (pt0) REVERT: B 94 LEU cc_start: 0.8418 (pp) cc_final: 0.7982 (tm) REVERT: B 110 ASN cc_start: 0.8124 (m110) cc_final: 0.7638 (t0) REVERT: B 126 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: C 1 MET cc_start: 0.6474 (tpp) cc_final: 0.5790 (tmt) REVERT: C 3 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 29 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7335 (m-70) REVERT: C 94 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7920 (pt) REVERT: C 104 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7686 (mm-30) REVERT: C 106 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7570 (mp0) REVERT: C 112 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7360 (mtm) REVERT: C 133 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: D 1 MET cc_start: 0.6202 (mtt) cc_final: 0.5926 (ptt) REVERT: D 31 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7769 (tp) REVERT: D 57 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8026 (ttmm) REVERT: D 61 LYS cc_start: 0.8353 (mttt) cc_final: 0.7625 (mptt) REVERT: D 64 LYS cc_start: 0.7783 (mttm) cc_final: 0.7105 (mmtt) REVERT: D 83 GLU cc_start: 0.7823 (tt0) cc_final: 0.7011 (mt-10) REVERT: D 102 GLU cc_start: 0.8039 (pp20) cc_final: 0.7793 (pp20) REVERT: D 113 MET cc_start: 0.8573 (mmm) cc_final: 0.8313 (mmm) REVERT: D 114 MET cc_start: 0.8354 (mtp) cc_final: 0.8100 (mtm) REVERT: D 126 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 129 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7675 (pt0) REVERT: D 140 LYS cc_start: 0.8433 (ttmp) cc_final: 0.7893 (ttpp) REVERT: D 254 GLN cc_start: 0.8481 (tt0) cc_final: 0.7801 (tt0) REVERT: E 94 LEU cc_start: 0.8695 (pt) cc_final: 0.8354 (mm) REVERT: E 104 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (mt-10) REVERT: E 112 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7802 (mmt) REVERT: E 123 GLU cc_start: 0.8067 (tp30) cc_final: 0.7800 (tt0) REVERT: E 212 MET cc_start: 0.8293 (mmm) cc_final: 0.7969 (mmp) REVERT: E 230 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7085 (pt0) REVERT: E 235 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7653 (tpp80) outliers start: 37 outliers final: 12 residues processed: 189 average time/residue: 0.6524 time to fit residues: 130.9121 Evaluate side-chains 187 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109298 restraints weight = 11387.282| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.15 r_work: 0.3148 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10372 Z= 0.117 Angle : 0.557 13.299 14014 Z= 0.277 Chirality : 0.042 0.274 1640 Planarity : 0.004 0.077 1763 Dihedral : 4.866 41.532 1371 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 16.00 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1312 helix: -0.39 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : 0.25 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 251 TYR 0.009 0.001 TYR C 145 PHE 0.015 0.001 PHE D 121 TRP 0.006 0.001 TRP F 16 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00277 (10372) covalent geometry : angle 0.55659 (14014) hydrogen bonds : bond 0.02867 ( 605) hydrogen bonds : angle 4.11510 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.369 Fit side-chains REVERT: A 57 LYS cc_start: 0.8490 (ttmm) cc_final: 0.7785 (tptt) REVERT: A 64 LYS cc_start: 0.7822 (mttm) cc_final: 0.7586 (ptmm) REVERT: A 68 LYS cc_start: 0.8684 (tttp) cc_final: 0.7884 (mptt) REVERT: A 113 MET cc_start: 0.8111 (mtm) cc_final: 0.7729 (mtp) REVERT: A 117 ASP cc_start: 0.8086 (m-30) cc_final: 0.7821 (m-30) REVERT: A 126 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: A 129 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7493 (tt0) REVERT: B 83 GLU cc_start: 0.7623 (tt0) cc_final: 0.7301 (pt0) REVERT: B 94 LEU cc_start: 0.8319 (pp) cc_final: 0.7916 (tm) REVERT: B 110 ASN cc_start: 0.8079 (m110) cc_final: 0.7561 (t0) REVERT: B 126 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: C 1 MET cc_start: 0.6413 (tpp) cc_final: 0.5743 (tmt) REVERT: C 3 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7887 (mp) REVERT: C 29 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: C 104 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7725 (mm-30) REVERT: C 106 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7645 (mp0) REVERT: C 112 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7385 (mtm) REVERT: C 133 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: D 1 MET cc_start: 0.6143 (mtt) cc_final: 0.5922 (ptt) REVERT: D 31 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7772 (tp) REVERT: D 57 LYS cc_start: 0.8281 (mtpt) cc_final: 0.8047 (ttmm) REVERT: D 61 LYS cc_start: 0.8325 (mttt) cc_final: 0.7902 (mtmm) REVERT: D 64 LYS cc_start: 0.7796 (mttm) cc_final: 0.7128 (mmtt) REVERT: D 83 GLU cc_start: 0.7825 (tt0) cc_final: 0.6995 (mt-10) REVERT: D 102 GLU cc_start: 0.8007 (pp20) cc_final: 0.7747 (pp20) REVERT: D 113 MET cc_start: 0.8591 (mmm) cc_final: 0.8327 (mmm) REVERT: D 114 MET cc_start: 0.8314 (mtp) cc_final: 0.8070 (mtm) REVERT: D 126 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8058 (mt-10) REVERT: D 129 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7652 (pt0) REVERT: D 140 LYS cc_start: 0.8321 (ttmp) cc_final: 0.7779 (ttpp) REVERT: D 254 GLN cc_start: 0.8488 (tt0) cc_final: 0.7714 (tt0) REVERT: E 94 LEU cc_start: 0.8658 (pt) cc_final: 0.8312 (tm) REVERT: E 104 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: E 112 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7886 (mmt) REVERT: E 123 GLU cc_start: 0.8046 (tp30) cc_final: 0.7834 (tt0) REVERT: E 212 MET cc_start: 0.8184 (mmm) cc_final: 0.7979 (mmp) REVERT: E 235 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7578 (tpp80) outliers start: 31 outliers final: 8 residues processed: 180 average time/residue: 0.6082 time to fit residues: 116.7984 Evaluate side-chains 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.0040 chunk 54 optimal weight: 0.4980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 29 HIS B 138 HIS C 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110748 restraints weight = 11344.138| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.23 r_work: 0.3187 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10372 Z= 0.096 Angle : 0.553 14.394 14014 Z= 0.267 Chirality : 0.041 0.291 1640 Planarity : 0.004 0.084 1763 Dihedral : 4.613 40.268 1371 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 17.30 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1312 helix: 0.10 (0.16), residues: 1061 sheet: None (None), residues: 0 loop : 0.32 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.007 0.001 TYR C 145 PHE 0.017 0.001 PHE A 36 TRP 0.008 0.001 TRP F 16 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00217 (10372) covalent geometry : angle 0.55261 (14014) hydrogen bonds : bond 0.02554 ( 605) hydrogen bonds : angle 3.92871 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.363 Fit side-chains REVERT: A 57 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7768 (tptt) REVERT: A 64 LYS cc_start: 0.7776 (mttm) cc_final: 0.7554 (ptmm) REVERT: A 68 LYS cc_start: 0.8638 (tttp) cc_final: 0.7795 (mptt) REVERT: A 113 MET cc_start: 0.8084 (mtm) cc_final: 0.7687 (mtp) REVERT: A 117 ASP cc_start: 0.8098 (m-30) cc_final: 0.7847 (m-30) REVERT: B 83 GLU cc_start: 0.7553 (tt0) cc_final: 0.7254 (pt0) REVERT: B 94 LEU cc_start: 0.8233 (pp) cc_final: 0.7924 (tm) REVERT: B 110 ASN cc_start: 0.7979 (m110) cc_final: 0.7310 (t0) REVERT: B 126 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: B 226 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7706 (ttpt) REVERT: C 1 MET cc_start: 0.6420 (tpp) cc_final: 0.5705 (tmt) REVERT: C 3 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7808 (mp) REVERT: C 29 HIS cc_start: 0.7720 (t70) cc_final: 0.7244 (m-70) REVERT: C 104 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7738 (mm-30) REVERT: C 106 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7592 (mp0) REVERT: C 112 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: C 133 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: D 31 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7748 (tp) REVERT: D 61 LYS cc_start: 0.8326 (mttt) cc_final: 0.8013 (mtpt) REVERT: D 64 LYS cc_start: 0.7772 (mttm) cc_final: 0.7105 (mmtt) REVERT: D 83 GLU cc_start: 0.7807 (tt0) cc_final: 0.7003 (mt-10) REVERT: D 102 GLU cc_start: 0.7978 (pp20) cc_final: 0.7747 (pp20) REVERT: D 113 MET cc_start: 0.8527 (mmm) cc_final: 0.8274 (mmm) REVERT: D 114 MET cc_start: 0.8249 (mtp) cc_final: 0.8005 (mtm) REVERT: D 129 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7576 (pt0) REVERT: D 140 LYS cc_start: 0.8279 (ttmp) cc_final: 0.7737 (ttpp) REVERT: D 254 GLN cc_start: 0.8463 (tt0) cc_final: 0.7667 (tt0) REVERT: E 94 LEU cc_start: 0.8593 (pt) cc_final: 0.8287 (tm) REVERT: E 104 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: E 112 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: E 113 MET cc_start: 0.7344 (tpt) cc_final: 0.7093 (tpp) REVERT: E 123 GLU cc_start: 0.8059 (tp30) cc_final: 0.7858 (tt0) REVERT: E 174 ASN cc_start: 0.7990 (t0) cc_final: 0.7696 (p0) outliers start: 22 outliers final: 4 residues processed: 175 average time/residue: 0.6505 time to fit residues: 121.0314 Evaluate side-chains 163 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 138 HIS C 254 GLN D 29 HIS D 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109019 restraints weight = 11270.023| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.22 r_work: 0.3161 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10372 Z= 0.111 Angle : 0.578 13.238 14014 Z= 0.278 Chirality : 0.042 0.322 1640 Planarity : 0.004 0.080 1763 Dihedral : 4.580 39.678 1371 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 1.48 % Allowed : 19.06 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1312 helix: 0.30 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : 0.38 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 251 TYR 0.009 0.001 TYR C 145 PHE 0.012 0.001 PHE B 149 TRP 0.020 0.001 TRP F 16 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00263 (10372) covalent geometry : angle 0.57804 (14014) hydrogen bonds : bond 0.02652 ( 605) hydrogen bonds : angle 3.89805 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.373 Fit side-chains REVERT: A 57 LYS cc_start: 0.8469 (ttmm) cc_final: 0.7771 (tptt) REVERT: A 68 LYS cc_start: 0.8600 (tttp) cc_final: 0.7820 (mptt) REVERT: A 113 MET cc_start: 0.8070 (mtm) cc_final: 0.7673 (mtp) REVERT: A 117 ASP cc_start: 0.8109 (m-30) cc_final: 0.7853 (m-30) REVERT: B 83 GLU cc_start: 0.7586 (tt0) cc_final: 0.7272 (pt0) REVERT: B 110 ASN cc_start: 0.7893 (m110) cc_final: 0.7376 (t0) REVERT: B 126 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: C 1 MET cc_start: 0.6256 (tpp) cc_final: 0.5636 (tmt) REVERT: C 3 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 29 HIS cc_start: 0.7735 (t70) cc_final: 0.7221 (m-70) REVERT: C 104 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7730 (mm-30) REVERT: C 106 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7616 (mp0) REVERT: C 112 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7366 (mtm) REVERT: C 133 GLU cc_start: 0.8234 (tt0) cc_final: 0.7999 (mt-10) REVERT: D 31 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7755 (tp) REVERT: D 61 LYS cc_start: 0.8309 (mttt) cc_final: 0.7761 (mmtt) REVERT: D 64 LYS cc_start: 0.7760 (mttm) cc_final: 0.7108 (mmtt) REVERT: D 83 GLU cc_start: 0.7812 (tt0) cc_final: 0.6997 (mt-10) REVERT: D 102 GLU cc_start: 0.8026 (pp20) cc_final: 0.7743 (pp20) REVERT: D 113 MET cc_start: 0.8548 (mmm) cc_final: 0.8296 (mmm) REVERT: D 114 MET cc_start: 0.8373 (mtp) cc_final: 0.8155 (mtm) REVERT: D 129 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7603 (pt0) REVERT: D 140 LYS cc_start: 0.8369 (ttmp) cc_final: 0.7833 (ttpp) REVERT: E 61 LYS cc_start: 0.8408 (mttm) cc_final: 0.7884 (mmtm) REVERT: E 94 LEU cc_start: 0.8542 (pt) cc_final: 0.8286 (tm) REVERT: E 104 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: E 112 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7904 (mmt) REVERT: E 123 GLU cc_start: 0.8049 (tp30) cc_final: 0.7818 (tt0) outliers start: 16 outliers final: 6 residues processed: 166 average time/residue: 0.6903 time to fit residues: 121.4540 Evaluate side-chains 163 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS E 174 ASN E 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109964 restraints weight = 11261.091| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.22 r_work: 0.3176 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10372 Z= 0.105 Angle : 0.570 12.961 14014 Z= 0.274 Chirality : 0.042 0.327 1640 Planarity : 0.005 0.083 1763 Dihedral : 4.507 39.796 1371 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 18.78 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1312 helix: 0.48 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : 0.49 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 251 TYR 0.009 0.001 TYR C 197 PHE 0.022 0.001 PHE A 36 TRP 0.018 0.001 TRP F 16 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00245 (10372) covalent geometry : angle 0.56957 (14014) hydrogen bonds : bond 0.02591 ( 605) hydrogen bonds : angle 3.83173 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.360 Fit side-chains REVERT: A 57 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7762 (tptt) REVERT: A 68 LYS cc_start: 0.8590 (tttp) cc_final: 0.7799 (mptt) REVERT: A 113 MET cc_start: 0.8053 (mtm) cc_final: 0.7692 (mtp) REVERT: A 117 ASP cc_start: 0.8104 (m-30) cc_final: 0.7850 (m-30) REVERT: B 83 GLU cc_start: 0.7570 (tt0) cc_final: 0.7269 (pt0) REVERT: B 110 ASN cc_start: 0.7878 (m110) cc_final: 0.7365 (t0) REVERT: B 126 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: C 1 MET cc_start: 0.6265 (tpp) cc_final: 0.5603 (tmt) REVERT: C 3 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 29 HIS cc_start: 0.7739 (t70) cc_final: 0.7212 (m-70) REVERT: C 104 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7731 (mm-30) REVERT: C 106 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7596 (mp0) REVERT: C 112 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7334 (mtm) REVERT: C 119 LYS cc_start: 0.7584 (mmtp) cc_final: 0.7217 (mmpt) REVERT: C 133 GLU cc_start: 0.8200 (tt0) cc_final: 0.7983 (mt-10) REVERT: D 1 MET cc_start: 0.6828 (ptt) cc_final: 0.6565 (ptm) REVERT: D 31 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 61 LYS cc_start: 0.8305 (mttt) cc_final: 0.7797 (mmtt) REVERT: D 64 LYS cc_start: 0.7764 (mttm) cc_final: 0.7116 (mmtt) REVERT: D 83 GLU cc_start: 0.7729 (tt0) cc_final: 0.6939 (mt-10) REVERT: D 102 GLU cc_start: 0.7988 (pp20) cc_final: 0.7745 (pp20) REVERT: D 113 MET cc_start: 0.8572 (mmm) cc_final: 0.8341 (mmm) REVERT: D 114 MET cc_start: 0.8296 (mtp) cc_final: 0.8073 (mtm) REVERT: D 129 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7517 (pt0) REVERT: D 140 LYS cc_start: 0.8353 (ttmp) cc_final: 0.7817 (ttpp) REVERT: D 254 GLN cc_start: 0.8485 (tt0) cc_final: 0.7661 (tt0) REVERT: E 61 LYS cc_start: 0.8374 (mttm) cc_final: 0.7928 (mmtm) REVERT: E 104 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: E 112 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7932 (mmt) REVERT: E 113 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7149 (tpp) outliers start: 18 outliers final: 7 residues processed: 169 average time/residue: 0.6817 time to fit residues: 122.3311 Evaluate side-chains 167 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 113 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS C 254 GLN E 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111832 restraints weight = 11217.489| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.21 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10372 Z= 0.111 Angle : 0.574 12.113 14014 Z= 0.279 Chirality : 0.043 0.350 1640 Planarity : 0.004 0.080 1763 Dihedral : 4.485 39.226 1371 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.67 % Allowed : 18.96 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1312 helix: 0.57 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : 0.53 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 251 TYR 0.009 0.001 TYR C 197 PHE 0.014 0.001 PHE D 84 TRP 0.016 0.001 TRP F 16 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00261 (10372) covalent geometry : angle 0.57384 (14014) hydrogen bonds : bond 0.02665 ( 605) hydrogen bonds : angle 3.83563 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.233 Fit side-chains REVERT: A 57 LYS cc_start: 0.8462 (ttmm) cc_final: 0.7780 (tptt) REVERT: A 68 LYS cc_start: 0.8617 (tttp) cc_final: 0.7810 (mptt) REVERT: A 113 MET cc_start: 0.8111 (mtm) cc_final: 0.7737 (mtp) REVERT: A 117 ASP cc_start: 0.8117 (m-30) cc_final: 0.7856 (m-30) REVERT: A 172 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7180 (tp) REVERT: B 83 GLU cc_start: 0.7592 (tt0) cc_final: 0.7303 (pt0) REVERT: B 110 ASN cc_start: 0.7908 (m110) cc_final: 0.7381 (t0) REVERT: B 126 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: C 1 MET cc_start: 0.6338 (tpp) cc_final: 0.5676 (tmt) REVERT: C 3 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7784 (mp) REVERT: C 29 HIS cc_start: 0.7737 (t70) cc_final: 0.7187 (m-70) REVERT: C 104 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7747 (mm-30) REVERT: C 106 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7604 (mp0) REVERT: C 112 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: C 119 LYS cc_start: 0.7596 (mmtp) cc_final: 0.7240 (mmpt) REVERT: D 31 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7768 (tp) REVERT: D 61 LYS cc_start: 0.8314 (mttt) cc_final: 0.7809 (mmtt) REVERT: D 64 LYS cc_start: 0.7781 (mttm) cc_final: 0.7133 (mmtt) REVERT: D 102 GLU cc_start: 0.8080 (pp20) cc_final: 0.7794 (pp20) REVERT: D 113 MET cc_start: 0.8611 (mmm) cc_final: 0.8395 (mmm) REVERT: D 114 MET cc_start: 0.8312 (mtp) cc_final: 0.8067 (mtm) REVERT: D 129 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7578 (pt0) REVERT: D 140 LYS cc_start: 0.8361 (ttmp) cc_final: 0.7827 (ttpp) REVERT: E 61 LYS cc_start: 0.8388 (mttm) cc_final: 0.7988 (mmtm) REVERT: E 104 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: E 112 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7925 (mmt) outliers start: 18 outliers final: 7 residues processed: 169 average time/residue: 0.6543 time to fit residues: 117.2843 Evaluate side-chains 167 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS D 254 GLN E 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107326 restraints weight = 11206.574| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.20 r_work: 0.3142 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10372 Z= 0.130 Angle : 0.608 12.340 14014 Z= 0.294 Chirality : 0.044 0.354 1640 Planarity : 0.005 0.084 1763 Dihedral : 4.597 40.300 1371 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 19.52 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.24), residues: 1312 helix: 0.54 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : 0.50 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 99 TYR 0.009 0.001 TYR C 197 PHE 0.019 0.002 PHE A 36 TRP 0.014 0.001 TRP F 16 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00314 (10372) covalent geometry : angle 0.60789 (14014) hydrogen bonds : bond 0.02841 ( 605) hydrogen bonds : angle 3.90477 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.372 Fit side-chains REVERT: A 57 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7772 (tptt) REVERT: A 68 LYS cc_start: 0.8600 (tttp) cc_final: 0.7806 (mptt) REVERT: A 113 MET cc_start: 0.8084 (mtm) cc_final: 0.7696 (mtp) REVERT: A 117 ASP cc_start: 0.8133 (m-30) cc_final: 0.7866 (m-30) REVERT: A 172 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7204 (tp) REVERT: B 83 GLU cc_start: 0.7623 (tt0) cc_final: 0.7294 (pt0) REVERT: B 110 ASN cc_start: 0.7899 (m110) cc_final: 0.7368 (t0) REVERT: B 126 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 172 LEU cc_start: 0.7480 (mt) cc_final: 0.7021 (mm) REVERT: C 1 MET cc_start: 0.6394 (tpp) cc_final: 0.5901 (tpt) REVERT: C 3 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7798 (mp) REVERT: C 29 HIS cc_start: 0.7778 (t70) cc_final: 0.7191 (m-70) REVERT: C 104 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7741 (mm-30) REVERT: C 106 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7608 (mp0) REVERT: C 112 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: C 119 LYS cc_start: 0.7633 (mmtp) cc_final: 0.7217 (mmpt) REVERT: D 1 MET cc_start: 0.7045 (ptt) cc_final: 0.6698 (pp-130) REVERT: D 31 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7771 (tp) REVERT: D 61 LYS cc_start: 0.8351 (mttt) cc_final: 0.7811 (mmtt) REVERT: D 64 LYS cc_start: 0.7757 (mttm) cc_final: 0.7107 (mmtt) REVERT: D 102 GLU cc_start: 0.8039 (pp20) cc_final: 0.7786 (pp20) REVERT: D 113 MET cc_start: 0.8612 (mmm) cc_final: 0.7663 (mmm) REVERT: D 114 MET cc_start: 0.8313 (mtp) cc_final: 0.8084 (mtm) REVERT: D 129 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7689 (pt0) REVERT: D 140 LYS cc_start: 0.8375 (ttmp) cc_final: 0.7840 (ttpp) REVERT: E 61 LYS cc_start: 0.8392 (mttm) cc_final: 0.7987 (mmtm) REVERT: E 104 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: E 112 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7900 (mmt) outliers start: 14 outliers final: 6 residues processed: 165 average time/residue: 0.6673 time to fit residues: 116.7842 Evaluate side-chains 167 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS D 254 GLN E 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109058 restraints weight = 11356.061| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.14 r_work: 0.3176 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10372 Z= 0.114 Angle : 0.592 12.826 14014 Z= 0.285 Chirality : 0.043 0.362 1640 Planarity : 0.005 0.081 1763 Dihedral : 4.516 38.718 1371 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.39 % Allowed : 19.80 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1312 helix: 0.70 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : 0.50 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 251 TYR 0.011 0.001 TYR C 197 PHE 0.017 0.001 PHE A 36 TRP 0.018 0.001 TRP G 16 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00268 (10372) covalent geometry : angle 0.59248 (14014) hydrogen bonds : bond 0.02684 ( 605) hydrogen bonds : angle 3.85389 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.87 seconds wall clock time: 61 minutes 48.70 seconds (3708.70 seconds total)