Starting phenix.real_space_refine on Sun Aug 24 16:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8q_20689/08_2025/6u8q_20689.map" } resolution = 4.67 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= 0.001 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: 7 Type Number sf(0) Gaussians P 94 5.49 5 Mg 4 5.21 5 S 76 5.16 5 C 13154 2.51 5 N 3736 2.21 5 O 4061 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21129 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2129 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2083 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 503 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "C" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2128 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2067 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "G" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 503 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1646 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "J" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1639 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1517 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1498 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DLU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DLU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.12, per 1000 atoms: 0.19 Number of scatterers: 21129 At special positions: 0 Unit cell: (165.24, 152.28, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 76 16.00 P 94 15.00 Mg 4 11.99 F 4 9.00 O 4061 8.00 N 3736 7.00 C 13154 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: 1.51 Conformation dependent library (CDL) restraints added in 784.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 22 sheets defined 45.4% alpha, 18.3% beta 40 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 27 removed outlier: 3.512A pdb=" N PHE A 26 " --> pdb=" O MET A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.563A pdb=" N ALA A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.515A pdb=" N THR A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.790A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.822A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.628A pdb=" N VAL A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.577A pdb=" N GLU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.662A pdb=" N ALA B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.564A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 122 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 147 through 166 removed outlier: 4.138A pdb=" N GLU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 186 Processing helix chain 'B' and resid 196 through 221 removed outlier: 3.996A pdb=" N ILE B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.583A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 3.512A pdb=" N THR C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 134 removed outlier: 3.692A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 166 Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.948A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.896A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.733A pdb=" N GLN D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 10 " --> pdb=" O ASP D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 29 through 39 removed outlier: 3.923A pdb=" N ALA D 33 " --> pdb=" O PRO D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.532A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 removed outlier: 3.663A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.222A pdb=" N VAL D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 196 through 221 removed outlier: 4.568A pdb=" N ASP D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 207 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 106 removed outlier: 3.657A pdb=" N THR I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 134 Processing helix chain 'I' and resid 154 through 166 removed outlier: 3.769A pdb=" N ILE I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY I 163 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 171 through 186 Processing helix chain 'I' and resid 195 through 219 removed outlier: 4.958A pdb=" N GLN I 214 " --> pdb=" O THR I 210 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 106 removed outlier: 3.633A pdb=" N THR J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 154 through 166 removed outlier: 4.188A pdb=" N ILE J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 162 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN J 164 " --> pdb=" O LYS J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 187 removed outlier: 3.837A pdb=" N ARG J 187 " --> pdb=" O HIS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 212 removed outlier: 3.696A pdb=" N VAL J 201 " --> pdb=" O GLY J 197 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 221 Processing helix chain 'J' and resid 270 through 275 removed outlier: 3.832A pdb=" N GLN J 274 " --> pdb=" O TYR J 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET J 275 " --> pdb=" O GLY J 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 3.800A pdb=" N THR K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 removed outlier: 3.722A pdb=" N LYS K 127 " --> pdb=" O SER K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 166 removed outlier: 3.604A pdb=" N MET K 154 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 160 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.749A pdb=" N ARG K 187 " --> pdb=" O HIS K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 209 Processing helix chain 'L' and resid 93 through 108 removed outlier: 3.615A pdb=" N THR L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 removed outlier: 3.599A pdb=" N LYS L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 166 removed outlier: 3.572A pdb=" N ASN L 155 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS L 160 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE L 161 " --> pdb=" O GLU L 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN L 164 " --> pdb=" O LYS L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 187 removed outlier: 3.816A pdb=" N ARG L 187 " --> pdb=" O HIS L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 209 removed outlier: 3.637A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN L 209 " --> pdb=" O ALA L 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 105 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 151 through 157 removed outlier: 3.610A pdb=" N LYS M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 185 removed outlier: 3.994A pdb=" N ALA M 175 " --> pdb=" O HIS M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 208 removed outlier: 3.978A pdb=" N VAL M 201 " --> pdb=" O GLY M 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 106 Processing helix chain 'N' and resid 123 through 132 Processing helix chain 'N' and resid 155 through 165 removed outlier: 4.130A pdb=" N GLY N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN N 164 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 165 " --> pdb=" O ILE N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'N' and resid 171 through 186 removed outlier: 3.631A pdb=" N ALA N 175 " --> pdb=" O HIS N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 210 removed outlier: 3.842A pdb=" N VAL N 201 " --> pdb=" O GLY N 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 106 Processing helix chain 'O' and resid 118 through 122 Processing helix chain 'O' and resid 123 through 132 Processing helix chain 'O' and resid 156 through 166 removed outlier: 3.624A pdb=" N ILE O 161 " --> pdb=" O GLU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 169 No H-bonds generated for 'chain 'O' and resid 167 through 169' Processing helix chain 'O' and resid 171 through 186 Processing helix chain 'O' and resid 195 through 210 removed outlier: 4.029A pdb=" N VAL O 201 " --> pdb=" O GLY O 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 106 Processing helix chain 'P' and resid 123 through 134 removed outlier: 3.541A pdb=" N LYS P 127 " --> pdb=" O SER P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 157 Processing helix chain 'P' and resid 171 through 186 removed outlier: 3.553A pdb=" N ALA P 175 " --> pdb=" O HIS P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 208 removed outlier: 4.401A pdb=" N VAL P 201 " --> pdb=" O GLY P 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 4.843A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 63 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 7.125A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 225 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 3.754A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TRP B 61 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 113 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 260 removed outlier: 6.645A pdb=" N VAL B 250 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL B 225 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 224 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 88 removed outlier: 4.141A pdb=" N LEU C 63 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL C 113 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 257 through 261 removed outlier: 7.233A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL C 225 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 84 through 89 removed outlier: 3.637A pdb=" N VAL D 72 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP D 61 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 113 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 225 through 228 removed outlier: 5.240A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP D 243 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 84 through 89 removed outlier: 4.312A pdb=" N VAL I 72 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP I 61 " --> pdb=" O HIS I 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 258 through 261 removed outlier: 7.799A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL I 225 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 84 through 89 removed outlier: 3.827A pdb=" N VAL J 72 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP J 61 " --> pdb=" O HIS J 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 257 through 261 removed outlier: 7.474A pdb=" N ALA J 248 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS J 244 " --> pdb=" O ALA J 248 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL J 250 " --> pdb=" O LEU J 242 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 224 " --> pdb=" O ILE J 268 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 84 through 89 removed outlier: 3.864A pdb=" N VAL K 72 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TRP K 61 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 84 through 89 removed outlier: 3.713A pdb=" N VAL L 72 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP L 61 " --> pdb=" O HIS L 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 85 through 88 removed outlier: 4.312A pdb=" N VAL M 113 " --> pdb=" O LYS M 136 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU M 138 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 257 through 261 removed outlier: 7.028A pdb=" N VAL M 250 " --> pdb=" O LEU M 242 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL M 225 " --> pdb=" O PRO M 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 61 through 68 removed outlier: 3.954A pdb=" N VAL N 72 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 112 through 113 removed outlier: 3.839A pdb=" N VAL N 113 " --> pdb=" O LYS N 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'O' and resid 84 through 89 removed outlier: 3.979A pdb=" N VAL O 72 " --> pdb=" O ILE O 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 61 through 68 Processing sheet with id=AC3, first strand: chain 'P' and resid 112 through 114 removed outlier: 4.245A pdb=" N VAL P 113 " --> pdb=" O LYS P 136 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU P 138 " --> pdb=" O VAL P 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'P' and resid 257 through 261 removed outlier: 7.104A pdb=" N VAL P 250 " --> pdb=" O LEU P 242 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL P 225 " --> pdb=" O PRO P 238 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3305 1.31 - 1.44: 6099 1.44 - 1.56: 12045 1.56 - 1.69: 192 1.69 - 1.82: 108 Bond restraints: 21749 Sorted by residual: bond pdb=" CBB DLU A 303 " pdb=" NBC DLU A 303 " ideal model delta sigma weight residual 1.453 1.641 -0.188 2.00e-02 2.50e+03 8.87e+01 bond pdb=" CBB DLU C 303 " pdb=" NBC DLU C 303 " ideal model delta sigma weight residual 1.453 1.641 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" CAW DLU A 303 " pdb=" CAY DLU A 303 " ideal model delta sigma weight residual 1.365 1.553 -0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" CAW DLU C 303 " pdb=" CAY DLU C 303 " ideal model delta sigma weight residual 1.365 1.552 -0.187 2.00e-02 2.50e+03 8.79e+01 bond pdb=" CAK DLU A 303 " pdb=" NBD DLU A 303 " ideal model delta sigma weight residual 1.327 1.504 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 21744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 29454 2.75 - 5.49: 302 5.49 - 8.24: 23 8.24 - 10.98: 7 10.98 - 13.73: 15 Bond angle restraints: 29801 Sorted by residual: angle pdb=" CA PRO P 233 " pdb=" N PRO P 233 " pdb=" CD PRO P 233 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 angle pdb=" CA PRO C 233 " pdb=" N PRO C 233 " pdb=" CD PRO C 233 " ideal model delta sigma weight residual 112.00 99.19 12.81 1.40e+00 5.10e-01 8.38e+01 angle pdb=" CA PRO J 233 " pdb=" N PRO J 233 " pdb=" CD PRO J 233 " ideal model delta sigma weight residual 112.00 99.20 12.80 1.40e+00 5.10e-01 8.35e+01 angle pdb=" CA PRO A 233 " pdb=" N PRO A 233 " pdb=" CD PRO A 233 " ideal model delta sigma weight residual 112.00 99.21 12.79 1.40e+00 5.10e-01 8.35e+01 angle pdb=" CA PRO M 233 " pdb=" N PRO M 233 " pdb=" CD PRO M 233 " ideal model delta sigma weight residual 112.00 99.21 12.79 1.40e+00 5.10e-01 8.35e+01 ... (remaining 29796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10864 17.87 - 35.74: 1091 35.74 - 53.61: 582 53.61 - 71.49: 164 71.49 - 89.36: 28 Dihedral angle restraints: 12729 sinusoidal: 5776 harmonic: 6953 Sorted by residual: dihedral pdb=" CA ILE M 84 " pdb=" C ILE M 84 " pdb=" N GLU M 85 " pdb=" CA GLU M 85 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LYS P 71 " pdb=" C LYS P 71 " pdb=" N VAL P 72 " pdb=" CA VAL P 72 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ALA M 205 " pdb=" C ALA M 205 " pdb=" N THR M 206 " pdb=" CA THR M 206 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 12726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2655 0.061 - 0.122: 578 0.122 - 0.183: 83 0.183 - 0.244: 3 0.244 - 0.305: 2 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CB ILE M 161 " pdb=" CA ILE M 161 " pdb=" CG1 ILE M 161 " pdb=" CG2 ILE M 161 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL N 165 " pdb=" CA VAL N 165 " pdb=" CG1 VAL N 165 " pdb=" CG2 VAL N 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1' DC G 38 " pdb=" O4' DC G 38 " pdb=" C2' DC G 38 " pdb=" N1 DC G 38 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 3318 not shown) Planarity restraints: 3442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO B 261 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 232 " 0.045 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO D 233 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 201 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C VAL I 201 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL I 201 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP I 202 " 0.012 2.00e-02 2.50e+03 ... (remaining 3439 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 151 2.56 - 3.14: 14659 3.14 - 3.73: 34399 3.73 - 4.31: 46495 4.31 - 4.90: 72961 Nonbonded interactions: 168665 Sorted by model distance: nonbonded pdb=" O ARG B 231 " pdb=" OD1 ASP B 232 " model vdw 1.972 3.040 nonbonded pdb=" O ARG M 231 " pdb=" OD1 ASP M 232 " model vdw 1.979 3.040 nonbonded pdb="MG MG A 301 " pdb=" OAE DLU A 303 " model vdw 2.007 2.170 nonbonded pdb=" O ARG J 231 " pdb=" OD1 ASP J 232 " model vdw 2.017 3.040 nonbonded pdb="MG MG C 302 " pdb=" OAE DLU C 303 " model vdw 2.059 2.170 ... (remaining 168660 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' and (resid 2 through 48 or resid 56 through 270)) selection = (chain 'B' and (resid 2 through 48 or resid 56 through 270)) selection = (chain 'C' and (resid 2 through 48 or resid 56 through 270)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 56 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 209 or resid 222 through 268)) selection = (chain 'J' and (resid 56 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 209 or resid 222 through 268)) selection = (chain 'M' and (resid 56 through 139 or resid 153 through 268)) selection = (chain 'P' and (resid 56 through 139 or resid 153 through 268)) } ncs_group { reference = (chain 'K' and (resid 56 through 139 or resid 153 through 209)) selection = (chain 'L' and (resid 56 through 139 or resid 153 through 209)) selection = (chain 'N' and resid 56 through 209) selection = (chain 'O' and resid 56 through 209) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.090 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 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 : 0.006 0.188 21749 Z= 0.299 Angle : 0.797 13.726 29801 Z= 0.462 Chirality : 0.051 0.305 3321 Planarity : 0.006 0.065 3442 Dihedral : 18.926 89.358 8255 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 4.07 % Allowed : 8.69 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.13), residues: 2394 helix: -2.63 (0.11), residues: 991 sheet: -2.07 (0.20), residues: 511 loop : -2.59 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.026 0.002 TYR M 99 PHE 0.011 0.001 PHE K 139 TRP 0.013 0.001 TRP N 108 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00572 (21749) covalent geometry : angle 0.79676 (29801) hydrogen bonds : bond 0.12929 ( 1054) hydrogen bonds : angle 6.78639 ( 2971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 246 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.7555 (mtm) cc_final: 0.7276 (ptp) REVERT: A 83 TYR cc_start: 0.7305 (t80) cc_final: 0.7088 (t80) REVERT: A 200 ILE cc_start: 0.8844 (tp) cc_final: 0.8492 (tp) REVERT: A 218 THR cc_start: 0.9293 (t) cc_final: 0.8835 (p) REVERT: B 158 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9252 (pp) REVERT: B 212 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: B 215 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8735 (tttt) REVERT: B 244 LYS cc_start: 0.9241 (tttt) cc_final: 0.8978 (ttmm) REVERT: C 22 MET cc_start: 0.7597 (mtm) cc_final: 0.7309 (ptp) REVERT: C 74 LEU cc_start: 0.8538 (mt) cc_final: 0.8177 (mt) REVERT: C 150 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8461 (t) REVERT: C 200 ILE cc_start: 0.9357 (tt) cc_final: 0.9016 (tp) REVERT: C 222 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.5321 (p0) REVERT: D 74 LEU cc_start: 0.8938 (tp) cc_final: 0.8685 (tp) REVERT: D 102 LEU cc_start: 0.8903 (tp) cc_final: 0.8697 (mt) REVERT: D 215 LYS cc_start: 0.8421 (mptt) cc_final: 0.7969 (ttmt) REVERT: D 259 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7108 (p) REVERT: I 208 ILE cc_start: 0.9085 (tp) cc_final: 0.8769 (pt) REVERT: J 213 LEU cc_start: 0.9043 (mt) cc_final: 0.8805 (mt) REVERT: J 231 ARG cc_start: 0.6824 (mtp180) cc_final: 0.6149 (tpt90) REVERT: K 102 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.5974 (mt) REVERT: K 154 MET cc_start: 0.8237 (mmt) cc_final: 0.8014 (mmm) REVERT: M 225 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (p) REVERT: M 230 SER cc_start: 0.6616 (OUTLIER) cc_final: 0.6409 (p) REVERT: N 69 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: O 102 LEU cc_start: -0.0853 (OUTLIER) cc_final: -0.1262 (tt) REVERT: P 226 TYR cc_start: 0.6899 (m-80) cc_final: 0.6527 (m-10) outliers start: 82 outliers final: 13 residues processed: 319 average time/residue: 0.1365 time to fit residues: 64.8797 Evaluate side-chains 137 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 62 GLN A 216 GLN B 155 ASN C 27 ASN C 216 GLN D 252 GLN I 120 ASN I 216 GLN J 168 GLN J 177 GLN K 67 HIS K 120 ASN N 78 HIS N 171 HIS N 177 GLN O 155 ASN ** O 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 183 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.115155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.086736 restraints weight = 158442.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082418 restraints weight = 99821.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.082583 restraints weight = 66670.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.082726 restraints weight = 48421.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082424 restraints weight = 40025.915| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21749 Z= 0.179 Angle : 0.634 8.105 29801 Z= 0.359 Chirality : 0.046 0.197 3321 Planarity : 0.005 0.046 3442 Dihedral : 20.112 79.526 3698 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.15), residues: 2394 helix: -1.06 (0.14), residues: 1022 sheet: -2.01 (0.21), residues: 499 loop : -2.05 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 107 TYR 0.026 0.002 TYR M 99 PHE 0.023 0.002 PHE N 181 TRP 0.048 0.001 TRP N 132 HIS 0.008 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00393 (21749) covalent geometry : angle 0.63397 (29801) hydrogen bonds : bond 0.05140 ( 1054) hydrogen bonds : angle 5.30938 ( 2971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8086 (t80) cc_final: 0.7388 (t80) REVERT: A 184 ASN cc_start: 0.8515 (m-40) cc_final: 0.8307 (t0) REVERT: B 22 MET cc_start: 0.7966 (mtt) cc_final: 0.7710 (mtt) REVERT: C 83 TYR cc_start: 0.8440 (t80) cc_final: 0.7915 (t80) REVERT: D 102 LEU cc_start: 0.9186 (tp) cc_final: 0.8908 (mt) REVERT: D 154 MET cc_start: 0.8185 (mtm) cc_final: 0.7930 (mtm) REVERT: D 215 LYS cc_start: 0.8470 (mptt) cc_final: 0.8170 (ttmt) REVERT: J 231 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6564 (tpt90) REVERT: J 268 ILE cc_start: 0.9108 (pt) cc_final: 0.8727 (mm) REVERT: K 154 MET cc_start: 0.8302 (mmt) cc_final: 0.8050 (mmm) REVERT: N 178 MET cc_start: 0.5189 (ptp) cc_final: 0.4936 (ptp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1209 time to fit residues: 26.2605 Evaluate side-chains 89 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 156 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 183 HIS C 9 GLN C 44 GLN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 HIS J 221 GLN K 137 GLN K 183 HIS L 67 HIS L 171 HIS M 114 HIS ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN N 114 HIS ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.109570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.082739 restraints weight = 164081.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.080900 restraints weight = 105196.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081216 restraints weight = 72162.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081064 restraints weight = 56822.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 82)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078934 restraints weight = 49327.051| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21749 Z= 0.268 Angle : 0.752 10.140 29801 Z= 0.422 Chirality : 0.049 0.214 3321 Planarity : 0.006 0.072 3442 Dihedral : 20.066 84.531 3698 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.15 % Allowed : 5.32 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.15), residues: 2394 helix: -0.91 (0.14), residues: 1027 sheet: -2.11 (0.21), residues: 469 loop : -2.06 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 107 TYR 0.049 0.002 TYR O 83 PHE 0.022 0.002 PHE O 181 TRP 0.031 0.002 TRP J 108 HIS 0.010 0.002 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00574 (21749) covalent geometry : angle 0.75203 (29801) hydrogen bonds : bond 0.06655 ( 1054) hydrogen bonds : angle 5.73639 ( 2971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 MET cc_start: 0.7993 (mtt) cc_final: 0.7362 (mtt) REVERT: B 227 TYR cc_start: 0.8821 (p90) cc_final: 0.8556 (p90) REVERT: C 22 MET cc_start: 0.8204 (ptp) cc_final: 0.7636 (ptt) REVERT: D 22 MET cc_start: 0.7966 (mtp) cc_final: 0.7580 (mmt) REVERT: D 154 MET cc_start: 0.8585 (mtm) cc_final: 0.8212 (mtm) REVERT: D 215 LYS cc_start: 0.8845 (mptt) cc_final: 0.8613 (ttmt) REVERT: I 178 MET cc_start: 0.7801 (mmp) cc_final: 0.7518 (mmm) REVERT: I 275 MET cc_start: 0.7523 (ptt) cc_final: 0.6976 (ppp) REVERT: J 231 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7698 (tpt170) REVERT: K 154 MET cc_start: 0.8395 (mmt) cc_final: 0.7877 (mmm) REVERT: K 167 ASP cc_start: 0.9053 (t0) cc_final: 0.8739 (p0) REVERT: O 181 PHE cc_start: 0.7225 (t80) cc_final: 0.6977 (t80) REVERT: P 227 TYR cc_start: 0.8811 (p90) cc_final: 0.8554 (p90) outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.1012 time to fit residues: 20.1146 Evaluate side-chains 75 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 198 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 GLN J 221 GLN M 171 HIS ** N 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.111995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.084678 restraints weight = 164189.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.080457 restraints weight = 103044.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.080515 restraints weight = 67400.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.080652 restraints weight = 50004.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080732 restraints weight = 40627.802| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21749 Z= 0.143 Angle : 0.582 7.827 29801 Z= 0.328 Chirality : 0.045 0.167 3321 Planarity : 0.004 0.051 3442 Dihedral : 19.979 89.466 3698 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.16), residues: 2394 helix: -0.29 (0.15), residues: 1017 sheet: -1.87 (0.22), residues: 448 loop : -1.87 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 199 TYR 0.016 0.001 TYR D 226 PHE 0.019 0.001 PHE N 181 TRP 0.012 0.001 TRP P 108 HIS 0.008 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00307 (21749) covalent geometry : angle 0.58245 (29801) hydrogen bonds : bond 0.04426 ( 1054) hydrogen bonds : angle 5.11591 ( 2971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8298 (t80) cc_final: 0.7538 (t80) REVERT: B 22 MET cc_start: 0.8300 (mtt) cc_final: 0.7881 (mtt) REVERT: C 83 TYR cc_start: 0.8451 (t80) cc_final: 0.8004 (t80) REVERT: D 215 LYS cc_start: 0.8714 (mptt) cc_final: 0.8455 (ttmt) REVERT: I 178 MET cc_start: 0.7722 (mmp) cc_final: 0.7384 (mmm) REVERT: I 275 MET cc_start: 0.7232 (ptt) cc_final: 0.6704 (ppp) REVERT: J 120 ASN cc_start: 0.5703 (p0) cc_final: 0.5334 (p0) REVERT: J 231 ARG cc_start: 0.8034 (mtp180) cc_final: 0.7478 (tpt90) REVERT: J 268 ILE cc_start: 0.9386 (pt) cc_final: 0.8790 (mm) REVERT: K 154 MET cc_start: 0.8185 (mmt) cc_final: 0.7774 (mmm) REVERT: K 167 ASP cc_start: 0.9169 (t0) cc_final: 0.8853 (p0) REVERT: O 181 PHE cc_start: 0.7228 (t80) cc_final: 0.6979 (t80) REVERT: P 227 TYR cc_start: 0.8866 (p90) cc_final: 0.8595 (p90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1066 time to fit residues: 20.5714 Evaluate side-chains 80 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 89 optimal weight: 3.9990 chunk 183 optimal weight: 0.0770 chunk 180 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN I 171 HIS J 221 GLN P 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.086601 restraints weight = 164973.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.083483 restraints weight = 146330.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.084277 restraints weight = 105086.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.084432 restraints weight = 71266.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084766 restraints weight = 67965.618| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21749 Z= 0.226 Angle : 0.669 9.123 29801 Z= 0.375 Chirality : 0.047 0.199 3321 Planarity : 0.004 0.046 3442 Dihedral : 20.012 83.591 3698 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.16), residues: 2394 helix: -0.37 (0.14), residues: 1028 sheet: -2.07 (0.21), residues: 504 loop : -1.90 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 199 TYR 0.020 0.002 TYR B 83 PHE 0.020 0.002 PHE O 181 TRP 0.017 0.002 TRP B 108 HIS 0.011 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00485 (21749) covalent geometry : angle 0.66936 (29801) hydrogen bonds : bond 0.05905 ( 1054) hydrogen bonds : angle 5.32430 ( 2971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.4146 (pmm) cc_final: 0.3860 (pmm) REVERT: B 22 MET cc_start: 0.8261 (mtt) cc_final: 0.7751 (mtt) REVERT: C 83 TYR cc_start: 0.8428 (t80) cc_final: 0.8188 (t80) REVERT: C 182 ILE cc_start: 0.9620 (mt) cc_final: 0.9393 (mt) REVERT: D 154 MET cc_start: 0.8635 (mtm) cc_final: 0.8263 (mtm) REVERT: D 215 LYS cc_start: 0.8911 (mptt) cc_final: 0.8671 (ttmt) REVERT: I 178 MET cc_start: 0.7734 (mmp) cc_final: 0.7353 (mmm) REVERT: J 120 ASN cc_start: 0.4868 (p0) cc_final: 0.4444 (p0) REVERT: J 275 MET cc_start: 0.7996 (mmp) cc_final: 0.7414 (ptt) REVERT: K 154 MET cc_start: 0.7901 (mmt) cc_final: 0.7427 (mmm) REVERT: K 167 ASP cc_start: 0.9152 (t0) cc_final: 0.8804 (p0) REVERT: P 227 TYR cc_start: 0.9014 (p90) cc_final: 0.8665 (p90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0931 time to fit residues: 15.1922 Evaluate side-chains 72 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081364 restraints weight = 165937.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.077804 restraints weight = 104311.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.078049 restraints weight = 70206.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.078161 restraints weight = 51775.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.078441 restraints weight = 42883.137| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21749 Z= 0.199 Angle : 0.646 8.393 29801 Z= 0.362 Chirality : 0.047 0.199 3321 Planarity : 0.004 0.055 3442 Dihedral : 20.095 87.047 3698 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.16), residues: 2394 helix: -0.17 (0.15), residues: 1014 sheet: -2.02 (0.22), residues: 492 loop : -1.71 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG O 107 TYR 0.013 0.002 TYR P 226 PHE 0.024 0.002 PHE A 185 TRP 0.017 0.002 TRP P 108 HIS 0.016 0.002 HIS J 114 Details of bonding type rmsd covalent geometry : bond 0.00427 (21749) covalent geometry : angle 0.64559 (29801) hydrogen bonds : bond 0.05125 ( 1054) hydrogen bonds : angle 5.30236 ( 2971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 MET cc_start: 0.8340 (mtt) cc_final: 0.7813 (mtt) REVERT: B 154 MET cc_start: 0.8344 (mtm) cc_final: 0.8096 (mtm) REVERT: C 182 ILE cc_start: 0.9573 (mt) cc_final: 0.9365 (mt) REVERT: D 22 MET cc_start: 0.8041 (mmt) cc_final: 0.7282 (mpp) REVERT: D 154 MET cc_start: 0.8492 (mtm) cc_final: 0.8247 (mtm) REVERT: D 215 LYS cc_start: 0.8854 (mptt) cc_final: 0.8645 (ttmt) REVERT: I 178 MET cc_start: 0.7840 (mmp) cc_final: 0.7582 (mmm) REVERT: J 275 MET cc_start: 0.7852 (mmp) cc_final: 0.7436 (ptt) REVERT: K 154 MET cc_start: 0.7908 (mmt) cc_final: 0.7210 (mmm) REVERT: P 123 SER cc_start: 0.4654 (m) cc_final: 0.4401 (t) REVERT: P 226 TYR cc_start: 0.7416 (m-10) cc_final: 0.6750 (m-10) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1160 time to fit residues: 19.7904 Evaluate side-chains 72 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 229 optimal weight: 0.0170 chunk 132 optimal weight: 8.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.110792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.084307 restraints weight = 163779.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.080236 restraints weight = 108023.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.079759 restraints weight = 72403.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.080063 restraints weight = 52294.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.080312 restraints weight = 41872.398| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21749 Z= 0.131 Angle : 0.569 7.723 29801 Z= 0.317 Chirality : 0.045 0.187 3321 Planarity : 0.004 0.049 3442 Dihedral : 19.942 89.940 3698 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2394 helix: 0.17 (0.15), residues: 1022 sheet: -1.85 (0.22), residues: 508 loop : -1.63 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.013 0.001 TYR A 83 PHE 0.032 0.001 PHE C 100 TRP 0.011 0.001 TRP D 108 HIS 0.018 0.001 HIS I 114 Details of bonding type rmsd covalent geometry : bond 0.00285 (21749) covalent geometry : angle 0.56853 (29801) hydrogen bonds : bond 0.04151 ( 1054) hydrogen bonds : angle 4.92710 ( 2971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 MET cc_start: 0.8240 (mtt) cc_final: 0.7780 (mtt) REVERT: B 154 MET cc_start: 0.8297 (mtm) cc_final: 0.7946 (mtm) REVERT: D 154 MET cc_start: 0.8440 (mtm) cc_final: 0.8093 (ptp) REVERT: D 215 LYS cc_start: 0.8849 (mptt) cc_final: 0.8603 (ttmt) REVERT: I 178 MET cc_start: 0.7771 (mmp) cc_final: 0.7498 (mmm) REVERT: J 275 MET cc_start: 0.7854 (mmp) cc_final: 0.7590 (ptt) REVERT: K 154 MET cc_start: 0.7948 (mmt) cc_final: 0.7282 (mmm) REVERT: L 154 MET cc_start: 0.8434 (mmp) cc_final: 0.8211 (mmm) REVERT: L 157 GLU cc_start: 0.8744 (tt0) cc_final: 0.8467 (mm-30) REVERT: P 123 SER cc_start: 0.4570 (m) cc_final: 0.4329 (t) REVERT: P 226 TYR cc_start: 0.7643 (m-10) cc_final: 0.6989 (m-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1094 time to fit residues: 19.9709 Evaluate side-chains 73 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 100 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 chunk 91 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 130 optimal weight: 0.0070 chunk 68 optimal weight: 7.9990 chunk 123 optimal weight: 0.1980 chunk 163 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN D 252 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.111487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083794 restraints weight = 163206.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.079871 restraints weight = 104133.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080117 restraints weight = 69368.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.080180 restraints weight = 48942.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080332 restraints weight = 40398.825| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21749 Z= 0.124 Angle : 0.551 7.134 29801 Z= 0.307 Chirality : 0.044 0.158 3321 Planarity : 0.003 0.046 3442 Dihedral : 19.817 87.371 3698 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2394 helix: 0.38 (0.16), residues: 1022 sheet: -1.69 (0.22), residues: 517 loop : -1.51 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 166 TYR 0.019 0.001 TYR D 83 PHE 0.021 0.001 PHE C 100 TRP 0.011 0.001 TRP B 108 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00268 (21749) covalent geometry : angle 0.55081 (29801) hydrogen bonds : bond 0.03806 ( 1054) hydrogen bonds : angle 4.76522 ( 2971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ILE cc_start: 0.9582 (mt) cc_final: 0.9378 (mt) REVERT: B 22 MET cc_start: 0.8379 (mtt) cc_final: 0.7910 (mtt) REVERT: B 154 MET cc_start: 0.8318 (mtm) cc_final: 0.7949 (mtm) REVERT: B 178 MET cc_start: 0.9168 (tpp) cc_final: 0.8950 (tpp) REVERT: C 83 TYR cc_start: 0.8515 (t80) cc_final: 0.8089 (t80) REVERT: C 178 MET cc_start: 0.9424 (mtm) cc_final: 0.9220 (mtm) REVERT: C 184 ASN cc_start: 0.9005 (m-40) cc_final: 0.8774 (t0) REVERT: D 22 MET cc_start: 0.8087 (mmt) cc_final: 0.6922 (mpp) REVERT: D 215 LYS cc_start: 0.8925 (mptt) cc_final: 0.8650 (ttmt) REVERT: I 178 MET cc_start: 0.7786 (mmp) cc_final: 0.7547 (mmm) REVERT: K 154 MET cc_start: 0.7956 (mmt) cc_final: 0.7249 (mmm) REVERT: L 154 MET cc_start: 0.8469 (mmp) cc_final: 0.8255 (mmm) REVERT: L 157 GLU cc_start: 0.8698 (tt0) cc_final: 0.8406 (mm-30) REVERT: P 123 SER cc_start: 0.4372 (m) cc_final: 0.4165 (t) REVERT: P 226 TYR cc_start: 0.7539 (m-80) cc_final: 0.6887 (m-10) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1028 time to fit residues: 19.1015 Evaluate side-chains 80 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 117 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 236 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.100970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.063670 restraints weight = 129132.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.064275 restraints weight = 87236.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065175 restraints weight = 65355.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065564 restraints weight = 52813.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.065808 restraints weight = 45360.724| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21749 Z= 0.210 Angle : 0.653 8.518 29801 Z= 0.363 Chirality : 0.046 0.221 3321 Planarity : 0.004 0.044 3442 Dihedral : 19.952 88.451 3698 Min Nonbonded Distance : 1.024 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2394 helix: 0.06 (0.15), residues: 1014 sheet: -1.79 (0.22), residues: 506 loop : -1.61 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 224 TYR 0.022 0.002 TYR D 83 PHE 0.028 0.002 PHE C 100 TRP 0.017 0.002 TRP D 108 HIS 0.007 0.002 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00452 (21749) covalent geometry : angle 0.65252 (29801) hydrogen bonds : bond 0.05515 ( 1054) hydrogen bonds : angle 5.12566 ( 2971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.4098 (pmm) cc_final: 0.3804 (pmm) REVERT: A 182 ILE cc_start: 0.9605 (mt) cc_final: 0.9357 (mt) REVERT: B 22 MET cc_start: 0.8349 (mtt) cc_final: 0.7882 (mtt) REVERT: B 154 MET cc_start: 0.8444 (mtm) cc_final: 0.8164 (mtm) REVERT: C 182 ILE cc_start: 0.9562 (mt) cc_final: 0.9336 (mt) REVERT: D 22 MET cc_start: 0.8118 (mmt) cc_final: 0.7059 (mpp) REVERT: D 215 LYS cc_start: 0.9050 (mptt) cc_final: 0.8749 (ttmt) REVERT: I 178 MET cc_start: 0.7387 (mmm) cc_final: 0.7124 (mmt) REVERT: N 178 MET cc_start: 0.6502 (ppp) cc_final: 0.6198 (ppp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1060 time to fit residues: 18.4528 Evaluate side-chains 65 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 199 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 84 optimal weight: 0.0770 chunk 204 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.066322 restraints weight = 137717.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.063837 restraints weight = 93895.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.064401 restraints weight = 66053.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.064677 restraints weight = 51894.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.064980 restraints weight = 43051.487| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21749 Z= 0.147 Angle : 0.581 7.145 29801 Z= 0.323 Chirality : 0.045 0.192 3321 Planarity : 0.004 0.048 3442 Dihedral : 19.961 87.026 3698 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.17), residues: 2394 helix: 0.30 (0.15), residues: 1021 sheet: -1.72 (0.22), residues: 502 loop : -1.59 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 224 TYR 0.014 0.001 TYR D 83 PHE 0.023 0.001 PHE C 100 TRP 0.011 0.001 TRP B 108 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00322 (21749) covalent geometry : angle 0.58106 (29801) hydrogen bonds : bond 0.04218 ( 1054) hydrogen bonds : angle 4.89620 ( 2971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ILE cc_start: 0.9610 (mt) cc_final: 0.9381 (mt) REVERT: B 22 MET cc_start: 0.8350 (mtt) cc_final: 0.7940 (mtt) REVERT: B 154 MET cc_start: 0.8409 (mtm) cc_final: 0.8091 (mtm) REVERT: D 22 MET cc_start: 0.8248 (mmt) cc_final: 0.7146 (mpp) REVERT: D 154 MET cc_start: 0.8399 (mtm) cc_final: 0.8161 (ptp) REVERT: D 215 LYS cc_start: 0.8999 (mptt) cc_final: 0.8797 (ttmt) REVERT: I 178 MET cc_start: 0.7380 (mmm) cc_final: 0.7141 (mmt) REVERT: I 275 MET cc_start: 0.8453 (mpp) cc_final: 0.7813 (ptt) REVERT: J 268 ILE cc_start: 0.9530 (pt) cc_final: 0.9113 (mp) REVERT: K 154 MET cc_start: 0.7918 (mmt) cc_final: 0.7259 (mmm) REVERT: M 135 ILE cc_start: -0.2507 (mt) cc_final: -0.2821 (mt) REVERT: N 178 MET cc_start: 0.6356 (ppp) cc_final: 0.6038 (ppp) REVERT: P 226 TYR cc_start: 0.7410 (m-80) cc_final: 0.6887 (m-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1061 time to fit residues: 19.2714 Evaluate side-chains 71 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 233 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063095 restraints weight = 129767.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.063779 restraints weight = 90395.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.064108 restraints weight = 65361.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.064617 restraints weight = 54329.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.064969 restraints weight = 47443.904| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 21749 Z= 0.220 Angle : 0.663 8.513 29801 Z= 0.370 Chirality : 0.047 0.197 3321 Planarity : 0.004 0.042 3442 Dihedral : 20.132 88.382 3698 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.16), residues: 2394 helix: 0.02 (0.15), residues: 1004 sheet: -1.81 (0.22), residues: 501 loop : -1.69 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 228 TYR 0.020 0.002 TYR P 226 PHE 0.027 0.002 PHE C 100 TRP 0.029 0.002 TRP K 132 HIS 0.006 0.002 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00472 (21749) covalent geometry : angle 0.66343 (29801) hydrogen bonds : bond 0.05605 ( 1054) hydrogen bonds : angle 5.20239 ( 2971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4732.89 seconds wall clock time: 82 minutes 10.35 seconds (4930.35 seconds total)