Starting phenix.real_space_refine on Sun Sep 13 05:30:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8q_20689/09_2026/6u8q_20689.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.86, per 1000 atoms: 0.23 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: 1.93 Conformation dependent library (CDL) restraints added in 882.7 milliseconds 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: 2.38 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: 3.58 Time building geometry restraints manager: 2.51 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: 29396 2.75 - 5.49: 359 5.49 - 8.24: 24 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: 2679 0.061 - 0.122: 569 0.122 - 0.183: 70 0.183 - 0.244: 1 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 2.43 2.23 0.20 2.00e-01 2.50e+01 1.01e+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: 4.570 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.490 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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= 0.383 Angle : 0.829 13.726 29801 Z= 0.584 Chirality : 0.049 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 are 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/Z covalent geometry : bond 0.00601 / 0.38 (21749) covalent geometry : angle 0.82932 / 0.58 (29801) hydrogen bonds : bond 0.12929 / 8.40 ( 1054) hydrogen bonds : angle 6.78639 / 4.73 ( 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 : 0.768 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: 0.7273 (ptp) REVERT: A 83 TYR cc_start: 0.7305 (t80) cc_final: 0.7087 (t80) REVERT: A 200 ILE cc_start: 0.8844 (tp) cc_final: 0.8493 (tp) REVERT: A 218 THR cc_start: 0.9294 (t) cc_final: 0.8836 (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: 0.8652 (tm-30) REVERT: B 215 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8736 (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: 0.8539 (mt) cc_final: 0.8177 (mt) REVERT: C 150 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8458 (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: 0.5320 (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: 0.7968 (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: 0.6151 (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: 0.6408 (p) REVERT: N 69 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: O 102 LEU cc_start: -0.0853 (OUTLIER) cc_final: -0.1263 (tt) REVERT: P 226 TYR cc_start: 0.6899 (m-80) cc_final: 0.6533 (m-10) outliers start: 82 outliers final: 13 residues processed: 319 average time/residue: 0.1662 time to fit residues: 79.7774 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 : 0.730 ------------------------------------------------------------------------------- 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... A 53 GLN A 62 GLN A 183 HIS A 216 GLN B 155 ASN C 27 ASN C 216 GLN I 120 ASN I 216 GLN J 168 GLN J 177 GLN K 120 ASN N 78 HIS N 171 HIS N 177 GLN O 114 HIS O 171 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.116380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088264 restraints weight = 157825.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.083810 restraints weight = 100319.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.083922 restraints weight = 66559.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.084057 restraints weight = 48932.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.084119 restraints weight = 38467.200| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21749 Z= 0.177 Angle : 0.685 10.443 29801 Z= 0.383 Chirality : 0.051 0.262 3321 Planarity : 0.005 0.067 3442 Dihedral : 20.542 81.922 3698 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.15 % Allowed : 3.18 % Favored : 96.67 % 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 are not related in a simple way. whole: -2.74 (0.15), residues: 2394 helix: -1.26 (0.14), residues: 1005 sheet: -1.94 (0.21), residues: 497 loop : -2.18 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 107 TYR 0.033 0.002 TYR M 99 PHE 0.027 0.002 PHE N 181 TRP 0.038 0.001 TRP N 132 HIS 0.007 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (21749) covalent geometry : angle 0.68525 / 0.38 (29801) hydrogen bonds : bond 0.05639 / 3.87 ( 1054) hydrogen bonds : angle 5.48950 / 3.85 ( 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 152 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.830 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: A 83 TYR cc_start: 0.7807 (t80) cc_final: 0.7200 (t80) REVERT: A 200 ILE cc_start: 0.9164 (tp) cc_final: 0.8881 (tp) REVERT: C 22 MET cc_start: 0.7973 (mtm) cc_final: 0.7745 (ptp) REVERT: C 63 LEU cc_start: 0.8201 (mt) cc_final: 0.7544 (tt) REVERT: C 83 TYR cc_start: 0.8240 (t80) cc_final: 0.7412 (t80) REVERT: D 102 LEU cc_start: 0.9072 (tp) cc_final: 0.8812 (mt) REVERT: D 212 GLU cc_start: 0.9246 (tp30) cc_final: 0.9001 (pt0) REVERT: D 215 LYS cc_start: 0.8416 (mptt) cc_final: 0.8114 (ttmt) REVERT: I 275 MET cc_start: 0.7755 (tpt) cc_final: 0.7507 (ppp) REVERT: J 231 ARG cc_start: 0.7349 (mtp180) cc_final: 0.6301 (tpt90) REVERT: N 178 MET cc_start: 0.5122 (ptp) cc_final: 0.4762 (ptp) outliers start: 3 outliers final: 0 residues processed: 152 average time/residue: 0.1580 time to fit residues: 37.6016 Evaluate side-chains 96 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 0.9980 chunk 136 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 156 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN C 9 GLN C 44 GLN D 252 GLN K 67 HIS L 67 HIS L 171 HIS M 252 GLN N 177 GLN O 155 ASN O 171 HIS ** P 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 183 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.114002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086036 restraints weight = 160041.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081440 restraints weight = 102396.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.081672 restraints weight = 67753.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081763 restraints weight = 51100.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.081545 restraints weight = 40957.996| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21749 Z= 0.197 Angle : 0.669 8.785 29801 Z= 0.376 Chirality : 0.049 0.265 3321 Planarity : 0.004 0.052 3442 Dihedral : 20.343 79.334 3698 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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 are not related in a simple way. whole: -2.30 (0.16), residues: 2394 helix: -0.72 (0.14), residues: 1024 sheet: -2.02 (0.21), residues: 500 loop : -2.00 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 199 TYR 0.033 0.002 TYR D 226 PHE 0.022 0.002 PHE N 181 TRP 0.021 0.001 TRP N 132 HIS 0.008 0.001 HIS P 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (21749) covalent geometry : angle 0.66898 / 0.38 (29801) hydrogen bonds : bond 0.05572 / 3.79 ( 1054) hydrogen bonds : angle 5.34763 / 3.76 ( 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 130 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.795 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: C 22 MET cc_start: 0.8205 (mtm) cc_final: 0.7821 (mtt) REVERT: C 83 TYR cc_start: 0.8212 (t80) cc_final: 0.7803 (t80) REVERT: D 102 LEU cc_start: 0.9207 (tp) cc_final: 0.8927 (mt) REVERT: D 215 LYS cc_start: 0.8574 (mptt) cc_final: 0.8296 (ttmt) REVERT: J 231 ARG cc_start: 0.7618 (mtp180) cc_final: 0.6611 (tpt90) REVERT: K 154 MET cc_start: 0.8191 (mmp) cc_final: 0.7831 (mmm) REVERT: K 155 ASN cc_start: 0.9057 (t0) cc_final: 0.8620 (p0) REVERT: N 200 ILE cc_start: -0.3060 (tt) cc_final: -0.3571 (tt) REVERT: O 181 PHE cc_start: 0.7436 (t80) cc_final: 0.7218 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1303 time to fit residues: 28.2043 Evaluate side-chains 83 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 8.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 81 optimal weight: 0.0030 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS M 171 HIS N 177 GLN O 171 HIS O 177 GLN ** P 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.112963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085300 restraints weight = 160681.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.081017 restraints weight = 103233.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.081049 restraints weight = 69791.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.081225 restraints weight = 51209.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.080908 restraints weight = 40174.181| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 21749 Z= 0.178 Angle : 0.656 12.509 29801 Z= 0.363 Chirality : 0.048 0.267 3321 Planarity : 0.004 0.065 3442 Dihedral : 20.242 89.001 3698 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % 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 are not related in a simple way. whole: -2.11 (0.16), residues: 2394 helix: -0.51 (0.15), residues: 1024 sheet: -2.07 (0.21), residues: 503 loop : -1.86 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 107 TYR 0.025 0.002 TYR B 227 PHE 0.023 0.002 PHE N 181 TRP 0.016 0.001 TRP B 108 HIS 0.007 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (21749) covalent geometry : angle 0.65557 / 0.36 (29801) hydrogen bonds : bond 0.05191 / 3.56 ( 1054) hydrogen bonds : angle 5.26009 / 3.70 ( 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 123 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASN cc_start: 0.8698 (t0) cc_final: 0.8342 (t0) REVERT: B 22 MET cc_start: 0.8102 (mtt) cc_final: 0.7851 (mtt) REVERT: C 22 MET cc_start: 0.8185 (mtm) cc_final: 0.7823 (mtt) REVERT: C 83 TYR cc_start: 0.8360 (t80) cc_final: 0.7853 (t80) REVERT: D 154 MET cc_start: 0.8394 (mtm) cc_final: 0.8146 (mtm) REVERT: D 178 MET cc_start: 0.9124 (tpp) cc_final: 0.8920 (tpp) REVERT: D 215 LYS cc_start: 0.8674 (mptt) cc_final: 0.8440 (ttmt) REVERT: I 178 MET cc_start: 0.7628 (mmp) cc_final: 0.7319 (mmm) REVERT: I 275 MET cc_start: 0.6984 (ptt) cc_final: 0.6583 (ppp) REVERT: J 231 ARG cc_start: 0.7855 (mtp180) cc_final: 0.6958 (tpt170) REVERT: K 154 MET cc_start: 0.8203 (mmp) cc_final: 0.7891 (mmm) REVERT: O 181 PHE cc_start: 0.7276 (t80) cc_final: 0.7028 (t80) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1301 time to fit residues: 26.9510 Evaluate side-chains 79 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 8.9990 chunk 180 optimal weight: 0.0170 chunk 156 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN D 252 GLN M 114 HIS ** M 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 171 HIS ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.114670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086925 restraints weight = 157499.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.082137 restraints weight = 101508.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082714 restraints weight = 65102.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 101)---------------| | r_work = 0.3729 r_free = 0.3729 target = 0.081106 restraints weight = 46486.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.081227 restraints weight = 41140.899| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 21749 Z= 0.121 Angle : 0.590 9.582 29801 Z= 0.327 Chirality : 0.047 0.250 3321 Planarity : 0.004 0.058 3442 Dihedral : 20.047 81.445 3698 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % 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 are not related in a simple way. whole: -1.70 (0.16), residues: 2394 helix: -0.15 (0.15), residues: 1023 sheet: -1.76 (0.21), residues: 497 loop : -1.74 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.035 0.001 TYR B 227 PHE 0.021 0.001 PHE N 181 TRP 0.014 0.001 TRP N 108 HIS 0.006 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (21749) covalent geometry : angle 0.58957 / 0.33 (29801) hydrogen bonds : bond 0.04188 / 2.86 ( 1054) hydrogen bonds : angle 4.96853 / 3.49 ( 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 127 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.951 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: A 184 ASN cc_start: 0.8537 (t0) cc_final: 0.8196 (t0) REVERT: B 22 MET cc_start: 0.8128 (mtt) cc_final: 0.7882 (mtt) REVERT: B 178 MET cc_start: 0.9184 (tpp) cc_final: 0.8933 (tpp) REVERT: B 227 TYR cc_start: 0.8429 (p90) cc_final: 0.8114 (p90) REVERT: B 240 LYS cc_start: 0.8903 (tptt) cc_final: 0.8659 (ttmt) REVERT: C 22 MET cc_start: 0.8094 (mtm) cc_final: 0.7759 (mtt) REVERT: C 83 TYR cc_start: 0.8318 (t80) cc_final: 0.7669 (t80) REVERT: D 102 LEU cc_start: 0.9167 (tp) cc_final: 0.8921 (mt) REVERT: D 215 LYS cc_start: 0.8651 (mptt) cc_final: 0.8399 (ttmt) REVERT: I 178 MET cc_start: 0.7605 (mmp) cc_final: 0.7293 (mmm) REVERT: I 275 MET cc_start: 0.7028 (ptt) cc_final: 0.6570 (ppp) REVERT: J 231 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7014 (tpt170) REVERT: K 154 MET cc_start: 0.8170 (mmp) cc_final: 0.7906 (mmm) REVERT: O 181 PHE cc_start: 0.7296 (t80) cc_final: 0.7042 (t80) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1329 time to fit residues: 28.5063 Evaluate side-chains 84 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 206 optimal weight: 50.0000 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 HIS K 137 GLN M 164 GLN ** M 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.114224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.086790 restraints weight = 159573.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.082319 restraints weight = 102678.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.082841 restraints weight = 68562.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.083110 restraints weight = 51444.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.083078 restraints weight = 41247.906| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21749 Z= 0.122 Angle : 0.575 10.078 29801 Z= 0.319 Chirality : 0.046 0.238 3321 Planarity : 0.003 0.040 3442 Dihedral : 19.941 84.474 3698 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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 are not related in a simple way. whole: -1.52 (0.16), residues: 2394 helix: 0.04 (0.15), residues: 1025 sheet: -1.75 (0.22), residues: 478 loop : -1.67 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 107 TYR 0.018 0.001 TYR O 83 PHE 0.020 0.001 PHE N 181 TRP 0.013 0.001 TRP B 108 HIS 0.006 0.001 HIS N 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (21749) covalent geometry : angle 0.57501 / 0.32 (29801) hydrogen bonds : bond 0.04257 / 2.92 ( 1054) hydrogen bonds : angle 4.89362 / 3.44 ( 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 116 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASN cc_start: 0.8557 (t0) cc_final: 0.8253 (t0) REVERT: B 22 MET cc_start: 0.8191 (mtt) cc_final: 0.7864 (mtt) REVERT: B 240 LYS cc_start: 0.8924 (tptt) cc_final: 0.8568 (ttmt) REVERT: C 22 MET cc_start: 0.8198 (mtm) cc_final: 0.7827 (mtt) REVERT: C 83 TYR cc_start: 0.8256 (t80) cc_final: 0.7699 (t80) REVERT: D 102 LEU cc_start: 0.9196 (tp) cc_final: 0.8956 (mt) REVERT: D 154 MET cc_start: 0.8496 (mtm) cc_final: 0.8265 (mtm) REVERT: D 215 LYS cc_start: 0.8705 (mptt) cc_final: 0.8449 (ttmt) REVERT: I 178 MET cc_start: 0.7766 (mmp) cc_final: 0.7501 (mmm) REVERT: J 120 ASN cc_start: 0.5800 (p0) cc_final: 0.5468 (p0) REVERT: J 231 ARG cc_start: 0.7889 (mtp180) cc_final: 0.7024 (tpt90) REVERT: K 154 MET cc_start: 0.8224 (mmp) cc_final: 0.7900 (mmm) REVERT: O 181 PHE cc_start: 0.7300 (t80) cc_final: 0.7049 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1333 time to fit residues: 26.2245 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 : 0.820 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 0.0030 chunk 27 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 164 optimal weight: 0.4980 chunk 190 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 229 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 HIS C 184 ASN D 252 GLN ** M 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 = 0.4130 r_free = 0.4130 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.086796 restraints weight = 162391.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.081880 restraints weight = 102749.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.082137 restraints weight = 67725.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082225 restraints weight = 49796.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.082388 restraints weight = 40022.841| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21749 Z= 0.108 Angle : 0.552 9.335 29801 Z= 0.305 Chirality : 0.046 0.212 3321 Planarity : 0.003 0.045 3442 Dihedral : 19.815 79.834 3698 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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 are not related in a simple way. whole: -1.33 (0.16), residues: 2394 helix: 0.22 (0.15), residues: 1026 sheet: -1.56 (0.22), residues: 495 loop : -1.65 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.020 0.001 TYR B 227 PHE 0.019 0.001 PHE N 181 TRP 0.013 0.001 TRP N 108 HIS 0.005 0.001 HIS N 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (21749) covalent geometry : angle 0.55181 / 0.30 (29801) hydrogen bonds : bond 0.03694 / 2.52 ( 1054) hydrogen bonds : angle 4.72310 / 3.32 ( 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 122 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.8535 (p0) cc_final: 0.8222 (t0) REVERT: A 184 ASN cc_start: 0.8503 (t0) cc_final: 0.8301 (t0) REVERT: B 22 MET cc_start: 0.8143 (mtt) cc_final: 0.7868 (mtt) REVERT: B 158 LEU cc_start: 0.9618 (mm) cc_final: 0.9354 (pp) REVERT: B 227 TYR cc_start: 0.8505 (p90) cc_final: 0.8188 (p90) REVERT: B 240 LYS cc_start: 0.8874 (tptt) cc_final: 0.8528 (ttmt) REVERT: C 22 MET cc_start: 0.8080 (mtm) cc_final: 0.7690 (mtt) REVERT: C 83 TYR cc_start: 0.8284 (t80) cc_final: 0.7827 (t80) REVERT: C 178 MET cc_start: 0.9275 (mtm) cc_final: 0.9070 (ptp) REVERT: C 184 ASN cc_start: 0.8354 (m110) cc_final: 0.7909 (t0) REVERT: D 22 MET cc_start: 0.7642 (mmt) cc_final: 0.6791 (mpp) REVERT: D 102 LEU cc_start: 0.9172 (tp) cc_final: 0.8906 (mt) REVERT: D 154 MET cc_start: 0.8418 (mtm) cc_final: 0.8161 (mtm) REVERT: D 215 LYS cc_start: 0.8622 (mptt) cc_final: 0.8372 (ttmt) REVERT: I 178 MET cc_start: 0.7735 (mmp) cc_final: 0.7405 (mmm) REVERT: J 120 ASN cc_start: 0.5849 (p0) cc_final: 0.5417 (p0) REVERT: J 231 ARG cc_start: 0.7922 (mtp180) cc_final: 0.6865 (tpt170) REVERT: K 154 MET cc_start: 0.8220 (mmp) cc_final: 0.7916 (mmm) REVERT: O 181 PHE cc_start: 0.7264 (t80) cc_final: 0.7018 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1377 time to fit residues: 28.2080 Evaluate side-chains 91 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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: 1.9990 chunk 177 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 163 optimal weight: 0.0170 chunk 114 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 overall best weight: 2.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS P 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.112121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.084713 restraints weight = 161847.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.080402 restraints weight = 102698.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.080349 restraints weight = 67916.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080485 restraints weight = 49959.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.080581 restraints weight = 39864.535| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21749 Z= 0.149 Angle : 0.595 9.414 29801 Z= 0.328 Chirality : 0.046 0.381 3321 Planarity : 0.004 0.037 3442 Dihedral : 19.842 88.806 3698 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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 are not related in a simple way. whole: -1.30 (0.17), residues: 2394 helix: 0.31 (0.15), residues: 1034 sheet: -1.73 (0.21), residues: 512 loop : -1.61 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.015 0.001 TYR O 83 PHE 0.017 0.001 PHE O 181 TRP 0.017 0.001 TRP B 108 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (21749) covalent geometry : angle 0.59474 / 0.33 (29801) hydrogen bonds : bond 0.04891 / 3.32 ( 1054) hydrogen bonds : angle 4.81027 / 3.39 ( 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 116 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASN cc_start: 0.8380 (t0) cc_final: 0.8084 (t0) REVERT: B 22 MET cc_start: 0.8183 (mtt) cc_final: 0.7836 (mtt) REVERT: B 178 MET cc_start: 0.9224 (tpp) cc_final: 0.8984 (mmm) REVERT: C 83 TYR cc_start: 0.8360 (t80) cc_final: 0.7772 (t80) REVERT: C 178 MET cc_start: 0.9363 (mtm) cc_final: 0.8945 (ptp) REVERT: C 182 ILE cc_start: 0.9554 (mt) cc_final: 0.9339 (mt) REVERT: C 184 ASN cc_start: 0.8545 (m110) cc_final: 0.8064 (t0) REVERT: D 102 LEU cc_start: 0.9231 (tp) cc_final: 0.8976 (mt) REVERT: D 215 LYS cc_start: 0.8704 (mptt) cc_final: 0.8496 (ttmt) REVERT: I 178 MET cc_start: 0.7790 (mmp) cc_final: 0.7534 (mmm) REVERT: J 120 ASN cc_start: 0.5807 (p0) cc_final: 0.5425 (p0) REVERT: J 231 ARG cc_start: 0.8095 (mtp180) cc_final: 0.6861 (tpt90) REVERT: K 154 MET cc_start: 0.8218 (mmp) cc_final: 0.7917 (mmm) REVERT: O 181 PHE cc_start: 0.7237 (t80) cc_final: 0.6998 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1337 time to fit residues: 26.1799 Evaluate side-chains 82 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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: 30.0000 chunk 185 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 43 optimal weight: 0.0010 chunk 236 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 83 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.114003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090611 restraints weight = 162757.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088604 restraints weight = 125432.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.089676 restraints weight = 85244.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.089719 restraints weight = 60556.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.089825 restraints weight = 58905.442| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21749 Z= 0.112 Angle : 0.555 8.810 29801 Z= 0.306 Chirality : 0.046 0.201 3321 Planarity : 0.003 0.040 3442 Dihedral : 19.723 82.438 3698 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 are not related in a simple way. whole: -1.19 (0.17), residues: 2394 helix: 0.36 (0.15), residues: 1026 sheet: -1.55 (0.22), residues: 476 loop : -1.58 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 166 TYR 0.017 0.001 TYR O 83 PHE 0.015 0.001 PHE N 181 TRP 0.026 0.001 TRP P 108 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (21749) covalent geometry : angle 0.55535 / 0.31 (29801) hydrogen bonds : bond 0.03769 / 2.56 ( 1054) hydrogen bonds : angle 4.69423 / 3.30 ( 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 115 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.838 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: 0.8160 (mtt) cc_final: 0.7850 (mtt) REVERT: B 158 LEU cc_start: 0.9635 (mm) cc_final: 0.9387 (pp) REVERT: B 178 MET cc_start: 0.9221 (tpp) cc_final: 0.8986 (mmm) REVERT: B 227 TYR cc_start: 0.8560 (p90) cc_final: 0.8294 (p90) REVERT: C 22 MET cc_start: 0.8229 (mtm) cc_final: 0.7582 (mtt) REVERT: C 83 TYR cc_start: 0.8377 (t80) cc_final: 0.7862 (t80) REVERT: C 178 MET cc_start: 0.9360 (mtm) cc_final: 0.8952 (ptp) REVERT: C 184 ASN cc_start: 0.8522 (m110) cc_final: 0.8033 (t0) REVERT: D 22 MET cc_start: 0.7712 (mmt) cc_final: 0.6726 (mpp) REVERT: D 154 MET cc_start: 0.8699 (mtm) cc_final: 0.8315 (mtm) REVERT: D 215 LYS cc_start: 0.8682 (mptt) cc_final: 0.8467 (ttmt) REVERT: I 178 MET cc_start: 0.7773 (mmp) cc_final: 0.7487 (mmm) REVERT: J 120 ASN cc_start: 0.5139 (p0) cc_final: 0.4619 (p0) REVERT: J 231 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7521 (ttt180) REVERT: K 154 MET cc_start: 0.8228 (mmp) cc_final: 0.7977 (mmm) REVERT: L 178 MET cc_start: 0.7426 (ptp) cc_final: 0.6926 (pmm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1435 time to fit residues: 27.4576 Evaluate side-chains 81 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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: 1.9990 chunk 139 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 63 optimal weight: 0.0060 chunk 199 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 194 optimal weight: 0.0980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN D 252 GLN M 67 HIS ** M 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 = 0.4122 r_free = 0.4122 target = 0.114320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.086195 restraints weight = 163266.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.081716 restraints weight = 102228.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 85)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081708 restraints weight = 66017.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.081808 restraints weight = 49496.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.081150 restraints weight = 37640.722| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21749 Z= 0.107 Angle : 0.542 8.636 29801 Z= 0.299 Chirality : 0.045 0.208 3321 Planarity : 0.003 0.040 3442 Dihedral : 19.645 81.438 3698 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 are not related in a simple way. whole: -1.05 (0.17), residues: 2394 helix: 0.45 (0.16), residues: 1026 sheet: -1.36 (0.22), residues: 472 loop : -1.56 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.016 0.001 TYR O 83 PHE 0.014 0.001 PHE N 181 TRP 0.018 0.001 TRP P 108 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (21749) covalent geometry : angle 0.54157 / 0.30 (29801) hydrogen bonds : bond 0.03673 / 2.50 ( 1054) hydrogen bonds : angle 4.61274 / 3.25 ( 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 113 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.801 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: B 22 MET cc_start: 0.8136 (mtt) cc_final: 0.7819 (mtt) REVERT: B 154 MET cc_start: 0.8443 (mtm) cc_final: 0.8174 (mtm) REVERT: B 158 LEU cc_start: 0.9595 (mm) cc_final: 0.9328 (pp) REVERT: B 178 MET cc_start: 0.9166 (tpp) cc_final: 0.8956 (mmm) REVERT: B 227 TYR cc_start: 0.8482 (p90) cc_final: 0.8215 (p90) REVERT: C 22 MET cc_start: 0.8262 (mtm) cc_final: 0.7567 (mtt) REVERT: C 83 TYR cc_start: 0.8166 (t80) cc_final: 0.7623 (t80) REVERT: C 184 ASN cc_start: 0.8350 (m110) cc_final: 0.7912 (t0) REVERT: D 22 MET cc_start: 0.7697 (mmt) cc_final: 0.6726 (mpp) REVERT: D 154 MET cc_start: 0.8422 (mtm) cc_final: 0.8169 (mtm) REVERT: D 215 LYS cc_start: 0.8684 (mptt) cc_final: 0.8484 (ttmt) REVERT: I 178 MET cc_start: 0.7740 (mmp) cc_final: 0.7512 (mmm) REVERT: J 120 ASN cc_start: 0.6164 (p0) cc_final: 0.5687 (p0) REVERT: J 231 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7595 (ttt180) REVERT: K 154 MET cc_start: 0.8280 (mmp) cc_final: 0.8006 (mmm) REVERT: L 178 MET cc_start: 0.7454 (ptp) cc_final: 0.7031 (pmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1317 time to fit residues: 25.4012 Evaluate side-chains 83 residues out of total 2021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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: 0.3980 chunk 116 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN B 252 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 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 = 0.4067 r_free = 0.4067 target = 0.111383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084028 restraints weight = 164597.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081083 restraints weight = 106537.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081426 restraints weight = 72912.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 81)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.081128 restraints weight = 52182.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081327 restraints weight = 43652.744| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 21749 Z= 0.179 Angle : 0.621 8.651 29801 Z= 0.342 Chirality : 0.046 0.212 3321 Planarity : 0.004 0.049 3442 Dihedral : 19.762 88.067 3698 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 are not related in a simple way. whole: -1.23 (0.17), residues: 2394 helix: 0.33 (0.15), residues: 1028 sheet: -1.66 (0.21), residues: 515 loop : -1.54 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 166 TYR 0.015 0.002 TYR O 83 PHE 0.028 0.002 PHE C 100 TRP 0.028 0.002 TRP P 108 HIS 0.008 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (21749) covalent geometry : angle 0.62120 / 0.34 (29801) hydrogen bonds : bond 0.05125 / 3.47 ( 1054) hydrogen bonds : angle 4.87654 / 3.42 ( 2971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.41 seconds wall clock time: 97 minutes 40.87 seconds (5860.87 seconds total)