Starting phenix.real_space_refine on Wed Aug 5 12:51:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.cif Found real_map, /net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30oe_57889/08_2026/30oe_57889.map" } resolution = 3.47 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= 0.004 sd= 0.048 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 6102 2.51 5 N 1649 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9719 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1608 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Chain: "B" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1608 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Chain: "C" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1608 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Chain: "D" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1607 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1608 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Chain: "F" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1608 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192} Chain breaks: 1 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1238 residue: pdb=" N MET A 1 " occ=0.35 ... (6 atoms not shown) pdb=" CE MET A 1 " occ=0.35 residue: pdb=" N PRO A 2 " occ=0.38 ... (5 atoms not shown) pdb=" CD PRO A 2 " occ=0.38 residue: pdb=" N ILE A 3 " occ=0.58 ... (6 atoms not shown) pdb=" CD1 ILE A 3 " occ=0.58 residue: pdb=" N VAL A 4 " occ=0.44 ... (5 atoms not shown) pdb=" CG2 VAL A 4 " occ=0.44 residue: pdb=" N GLN A 5 " occ=0.45 ... (7 atoms not shown) pdb=" NE2 GLN A 5 " occ=0.45 residue: pdb=" N ASN A 6 " occ=0.30 ... (6 atoms not shown) pdb=" ND2 ASN A 6 " occ=0.30 residue: pdb=" N LEU A 7 " occ=0.41 ... (6 atoms not shown) pdb=" CD2 LEU A 7 " occ=0.41 residue: pdb=" N GLN A 8 " occ=0.51 ... (7 atoms not shown) pdb=" NE2 GLN A 8 " occ=0.51 residue: pdb=" N GLY A 9 " occ=0.34 ... (2 atoms not shown) pdb=" O GLY A 9 " occ=0.34 residue: pdb=" N GLN A 10 " occ=0.44 ... (7 atoms not shown) pdb=" NE2 GLN A 10 " occ=0.44 residue: pdb=" N MET A 11 " occ=0.39 ... (6 atoms not shown) pdb=" CE MET A 11 " occ=0.39 residue: pdb=" N VAL A 12 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 VAL A 12 " occ=0.40 ... (remaining 1226 not shown) Time building chain proxies: 2.04, per 1000 atoms: 0.21 Number of scatterers: 9719 At special positions: 0 Unit cell: (117.7, 115.5, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 1878 8.00 N 1649 7.00 C 6102 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 414.9 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 69.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 17 through 31 removed outlier: 3.746A pdb=" N VAL A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 4.110A pdb=" N MET A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 63 through 83 removed outlier: 4.263A pdb=" N MET A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.567A pdb=" N GLN A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 146 removed outlier: 3.973A pdb=" N TRP A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.994A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.815A pdb=" N TRP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.618A pdb=" N THR A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.619A pdb=" N MET A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.502A pdb=" N ALA B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 45 removed outlier: 3.767A pdb=" N MET B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.662A pdb=" N THR B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.725A pdb=" N MET B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 Processing helix chain 'B' and resid 126 through 146 removed outlier: 3.875A pdb=" N TRP B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.806A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.729A pdb=" N TRP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 189 " --> pdb=" O TRP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.603A pdb=" N THR B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.811A pdb=" N CYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 31 removed outlier: 3.552A pdb=" N LEU C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN C 22 " --> pdb=" O PRO C 18 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 removed outlier: 3.859A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 63 through 84 removed outlier: 3.698A pdb=" N MET C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.669A pdb=" N TRP C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 161 through 176 removed outlier: 3.980A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 removed outlier: 4.045A pdb=" N TRP C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.627A pdb=" N ASN C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 4.335A pdb=" N ILE C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.573A pdb=" N MET C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 45 removed outlier: 4.108A pdb=" N MET D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 63 through 83 removed outlier: 3.823A pdb=" N MET D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.977A pdb=" N LYS D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 176 removed outlier: 3.867A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 removed outlier: 3.766A pdb=" N TRP D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 4.172A pdb=" N ILE D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.597A pdb=" N MET D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 removed outlier: 3.987A pdb=" N VAL E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 49 through 59 removed outlier: 3.582A pdb=" N THR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.722A pdb=" N MET E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 71 " --> pdb=" O MET E 67 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 126 through 146 removed outlier: 3.860A pdb=" N TRP E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 176 removed outlier: 4.044A pdb=" N ARG E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 194 removed outlier: 3.716A pdb=" N TRP E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 removed outlier: 4.125A pdb=" N ILE E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 206 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.505A pdb=" N MET E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS E 219 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.907A pdb=" N VAL F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 45 removed outlier: 3.899A pdb=" N MET F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 59 Processing helix chain 'F' and resid 63 through 84 removed outlier: 3.603A pdb=" N LEU F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 Processing helix chain 'F' and resid 126 through 146 removed outlier: 3.646A pdb=" N TRP F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 144 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 removed outlier: 3.928A pdb=" N ARG F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 194 removed outlier: 3.915A pdb=" N TRP F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 removed outlier: 3.973A pdb=" N ILE F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU F 206 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.532A pdb=" N CYS F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 5 483 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3185 1.34 - 1.46: 1065 1.46 - 1.57: 5505 1.57 - 1.69: 12 1.69 - 1.81: 144 Bond restraints: 9911 Sorted by residual: bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.36e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.32e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.27e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.09e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.81e+00 ... (remaining 9906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 13244 2.02 - 4.05: 197 4.05 - 6.07: 24 6.07 - 8.09: 3 8.09 - 10.12: 6 Bond angle restraints: 13474 Sorted by residual: angle pdb=" C ALA A 32 " pdb=" CA ALA A 32 " pdb=" CB ALA A 32 " ideal model delta sigma weight residual 117.23 111.13 6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" C ALA C 32 " pdb=" CA ALA C 32 " pdb=" CB ALA C 32 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 angle pdb=" C ALA D 32 " pdb=" CA ALA D 32 " pdb=" CB ALA D 32 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C2 IHP F 301 " pdb=" C1 IHP F 301 " pdb=" C6 IHP F 301 " ideal model delta sigma weight residual 110.87 120.99 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C4 IHP F 301 " pdb=" C5 IHP F 301 " pdb=" C6 IHP F 301 " ideal model delta sigma weight residual 109.60 118.78 -9.18 3.00e+00 1.11e-01 9.37e+00 ... (remaining 13469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.87: 5303 19.87 - 39.75: 603 39.75 - 59.62: 129 59.62 - 79.50: 33 79.50 - 99.37: 27 Dihedral angle restraints: 6095 sinusoidal: 2543 harmonic: 3552 Sorted by residual: dihedral pdb=" C5 IHP F 301 " pdb=" C3 IHP F 301 " pdb=" C4 IHP F 301 " pdb=" O13 IHP F 301 " ideal model delta sinusoidal sigma weight residual 186.74 87.37 99.37 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" C2 IHP F 301 " pdb=" C3 IHP F 301 " pdb=" C4 IHP F 301 " pdb=" C5 IHP F 301 " ideal model delta sinusoidal sigma weight residual -61.64 37.68 -99.32 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" O13 IHP F 301 " pdb=" C3 IHP F 301 " pdb=" C4 IHP F 301 " pdb=" O14 IHP F 301 " ideal model delta sinusoidal sigma weight residual 50.83 146.96 -96.13 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1258 0.050 - 0.099: 212 0.099 - 0.149: 50 0.149 - 0.198: 2 0.198 - 0.248: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C6 IHP F 301 " pdb=" C1 IHP F 301 " pdb=" C5 IHP F 301 " pdb=" O16 IHP F 301 " both_signs ideal model delta sigma weight residual False -2.50 -2.25 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C4 IHP F 301 " pdb=" C3 IHP F 301 " pdb=" C5 IHP F 301 " pdb=" O14 IHP F 301 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1521 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 185 " -0.013 2.00e-02 2.50e+03 1.07e-02 2.88e+00 pdb=" CG TRP E 185 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP E 185 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP E 185 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 185 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 185 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 185 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 185 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 185 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 185 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 17 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO E 18 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 18 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 18 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 19 " 0.130 9.50e-02 1.11e+02 5.85e-02 2.22e+00 pdb=" NE ARG F 19 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG F 19 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 19 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 19 " 0.003 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 146 2.69 - 3.25: 10215 3.25 - 3.80: 14232 3.80 - 4.35: 18100 4.35 - 4.90: 30112 Nonbonded interactions: 72805 Sorted by model distance: nonbonded pdb=" NE ARG C 19 " pdb=" O43 IHP C 301 " model vdw 2.142 2.496 nonbonded pdb=" NH2 ARG C 19 " pdb=" O43 IHP C 301 " model vdw 2.199 2.496 nonbonded pdb=" O GLN B 180 " pdb=" OD1 ASN B 184 " model vdw 2.285 3.040 nonbonded pdb=" O ASP F 153 " pdb=" OD1 ASP F 153 " model vdw 2.300 3.040 nonbonded pdb=" O GLN D 180 " pdb=" OD1 ASN D 184 " model vdw 2.374 3.040 ... (remaining 72800 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 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH2)) \ or resid 84 through 223)) selection = (chain 'B' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH2)) \ or resid 84 through 223)) selection = (chain 'C' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH2)) \ or resid 84 through 223)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH2)) \ or resid 84 through 223)) selection = (chain 'F' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH2)) \ or resid 84 through 223)) } 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=0.27 max=0.70 mean=0.48 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.004 0.029 9912 Z= 0.160 Angle : 0.637 10.116 13474 Z= 0.321 Chirality : 0.041 0.248 1524 Planarity : 0.004 0.058 1728 Dihedral : 18.786 99.371 3791 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.46 % Allowed : 17.14 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.22 (0.25), residues: 1212 helix: -0.05 (0.20), residues: 708 sheet: -1.51 (0.67), residues: 66 loop : 0.24 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.007 0.001 TYR A 170 PHE 0.009 0.001 PHE C 169 TRP 0.029 0.001 TRP E 185 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9911) covalent geometry : angle 0.63693 / 0.32 (13474) hydrogen bonds : bond 0.17733 / 12.36 ( 483) hydrogen bonds : angle 5.62363 / 3.87 ( 1443) Misc. bond : bond 0.00114 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.360 Fit side-chains REVERT: A 22 ASN cc_start: 0.8878 (t0) cc_final: 0.8406 (m-40) REVERT: A 26 LYS cc_start: 0.8360 (tttm) cc_final: 0.7921 (mmtp) REVERT: A 31 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7674 (mttt) REVERT: A 63 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7354 (p90) REVERT: A 64 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8246 (mm-40) REVERT: A 80 GLU cc_start: 0.7753 (tp30) cc_final: 0.7152 (mm-30) REVERT: A 118 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: A 139 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 31 LYS cc_start: 0.8208 (mptt) cc_final: 0.7347 (mttt) REVERT: B 80 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: B 153 ASP cc_start: 0.7807 (t70) cc_final: 0.7554 (t0) REVERT: C 31 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7703 (mttt) REVERT: C 80 GLU cc_start: 0.7759 (tp30) cc_final: 0.7313 (tp30) REVERT: C 119 MET cc_start: 0.8373 (mtp) cc_final: 0.8134 (mtp) REVERT: D 31 LYS cc_start: 0.7832 (tppp) cc_final: 0.7262 (mttt) REVERT: E 31 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7469 (mttt) REVERT: E 141 LYS cc_start: 0.7945 (tttm) cc_final: 0.7628 (ttmm) REVERT: F 31 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7683 (mttt) REVERT: F 80 GLU cc_start: 0.7392 (tp30) cc_final: 0.6812 (mm-30) REVERT: F 198 ASP cc_start: 0.7750 (t0) cc_final: 0.7430 (t0) REVERT: F 200 LYS cc_start: 0.6809 (tptt) cc_final: 0.6491 (tttm) outliers start: 26 outliers final: 18 residues processed: 215 average time/residue: 0.1062 time to fit residues: 30.4923 Evaluate side-chains 210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.180639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.137202 restraints weight = 11683.802| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.21 r_work: 0.3295 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 0.70 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 0.74 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (21 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9912 Z= 0.125 Angle : 0.599 10.077 13474 Z= 0.291 Chirality : 0.044 0.375 1524 Planarity : 0.004 0.028 1728 Dihedral : 14.857 99.631 1424 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.41 % Allowed : 16.10 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.32 (0.25), residues: 1212 helix: 0.28 (0.20), residues: 702 sheet: -1.45 (0.64), residues: 66 loop : 0.71 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 155 TYR 0.007 0.001 TYR E 131 PHE 0.008 0.001 PHE B 33 TRP 0.021 0.001 TRP E 185 HIS 0.005 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9911) covalent geometry : angle 0.59914 / 0.29 (13474) hydrogen bonds : bond 0.04571 / 3.07 ( 483) hydrogen bonds : angle 4.19330 / 2.94 ( 1443) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8613 (t0) cc_final: 0.8204 (m-40) REVERT: A 26 LYS cc_start: 0.8480 (tttm) cc_final: 0.7997 (mmtp) REVERT: A 31 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7619 (mttt) REVERT: A 80 GLU cc_start: 0.7805 (tp30) cc_final: 0.7114 (mm-30) REVERT: A 119 MET cc_start: 0.8436 (mtp) cc_final: 0.8160 (mtp) REVERT: A 215 MET cc_start: 0.6956 (mpp) cc_final: 0.6642 (mtt) REVERT: B 31 LYS cc_start: 0.7999 (mptt) cc_final: 0.7134 (mttt) REVERT: B 80 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: B 153 ASP cc_start: 0.7858 (t70) cc_final: 0.7588 (t0) REVERT: B 198 ASP cc_start: 0.7648 (t0) cc_final: 0.7408 (t0) REVERT: C 139 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 185 TRP cc_start: 0.5893 (t60) cc_final: 0.5232 (t60) REVERT: C 198 ASP cc_start: 0.7800 (t0) cc_final: 0.7387 (t0) REVERT: D 31 LYS cc_start: 0.7628 (tppp) cc_final: 0.7053 (mttt) REVERT: D 198 ASP cc_start: 0.7664 (t0) cc_final: 0.7458 (t0) REVERT: D 200 LYS cc_start: 0.6637 (tptt) cc_final: 0.6349 (tttp) REVERT: E 31 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7359 (mttt) REVERT: E 57 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8623 (mp) REVERT: E 141 LYS cc_start: 0.8098 (tttm) cc_final: 0.7848 (ttmm) REVERT: E 177 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5460 (tp40) REVERT: F 31 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7669 (mttt) REVERT: F 80 GLU cc_start: 0.7506 (tp30) cc_final: 0.7025 (mm-30) REVERT: F 139 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8133 (mt) REVERT: F 198 ASP cc_start: 0.7851 (t0) cc_final: 0.7489 (t0) REVERT: F 200 LYS cc_start: 0.6993 (tptt) cc_final: 0.6770 (tttm) outliers start: 36 outliers final: 21 residues processed: 218 average time/residue: 0.0951 time to fit residues: 28.1986 Evaluate side-chains 208 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 116 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN C 13 HIS ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135613 restraints weight = 11812.732| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.05 r_work: 0.3291 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 0.74 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 0.75 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (17 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9912 Z= 0.116 Angle : 0.586 10.442 13474 Z= 0.279 Chirality : 0.043 0.346 1524 Planarity : 0.004 0.031 1728 Dihedral : 13.752 97.191 1401 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.94 % Allowed : 17.23 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.37 (0.25), residues: 1212 helix: 0.23 (0.20), residues: 762 sheet: None (None), residues: 0 loop : 0.60 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 19 TYR 0.006 0.001 TYR C 131 PHE 0.006 0.001 PHE D 33 TRP 0.022 0.001 TRP E 185 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9911) covalent geometry : angle 0.58592 / 0.28 (13474) hydrogen bonds : bond 0.04025 / 2.68 ( 483) hydrogen bonds : angle 3.95321 / 2.79 ( 1443) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8478 (t0) cc_final: 0.8070 (m-40) REVERT: A 26 LYS cc_start: 0.8447 (tttm) cc_final: 0.7982 (mmtp) REVERT: A 80 GLU cc_start: 0.7827 (tp30) cc_final: 0.7108 (mm-30) REVERT: A 121 HIS cc_start: 0.7173 (t70) cc_final: 0.6923 (t-90) REVERT: A 198 ASP cc_start: 0.7705 (t0) cc_final: 0.7476 (t0) REVERT: A 215 MET cc_start: 0.6948 (mpp) cc_final: 0.6606 (mtt) REVERT: B 31 LYS cc_start: 0.7960 (mptt) cc_final: 0.7199 (mttt) REVERT: B 80 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: B 153 ASP cc_start: 0.7861 (t70) cc_final: 0.7597 (t0) REVERT: C 14 GLN cc_start: 0.7577 (mt0) cc_final: 0.7274 (mp10) REVERT: C 139 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8434 (mt) REVERT: C 185 TRP cc_start: 0.6058 (t60) cc_final: 0.5390 (t60) REVERT: C 198 ASP cc_start: 0.7737 (t0) cc_final: 0.7282 (t0) REVERT: D 31 LYS cc_start: 0.7698 (tppp) cc_final: 0.7095 (mttt) REVERT: D 200 LYS cc_start: 0.6747 (tptt) cc_final: 0.6497 (tttp) REVERT: E 11 MET cc_start: 0.6325 (tmm) cc_final: 0.5888 (ppp) REVERT: E 31 LYS cc_start: 0.7660 (mmtm) cc_final: 0.7263 (mttt) REVERT: E 141 LYS cc_start: 0.8117 (tttm) cc_final: 0.7831 (ttmm) REVERT: E 177 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5206 (tp40) REVERT: F 31 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7622 (mttt) REVERT: F 80 GLU cc_start: 0.7422 (tp30) cc_final: 0.7041 (mm-30) REVERT: F 139 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8082 (mt) REVERT: F 198 ASP cc_start: 0.7765 (t0) cc_final: 0.7546 (t0) REVERT: F 202 ILE cc_start: 0.7713 (mt) cc_final: 0.7507 (tt) outliers start: 31 outliers final: 21 residues processed: 218 average time/residue: 0.1043 time to fit residues: 30.5876 Evaluate side-chains 211 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132127 restraints weight = 11980.797| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.24 r_work: 0.3218 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 0.75 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 0.75 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9912 Z= 0.177 Angle : 0.655 10.904 13474 Z= 0.314 Chirality : 0.046 0.350 1524 Planarity : 0.005 0.032 1728 Dihedral : 13.376 94.433 1398 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.11 % Allowed : 17.42 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.25), residues: 1212 helix: 0.20 (0.20), residues: 726 sheet: None (None), residues: 0 loop : 0.27 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 144 TYR 0.008 0.001 TYR A 170 PHE 0.012 0.002 PHE D 169 TRP 0.024 0.002 TRP F 185 HIS 0.006 0.001 HIS C 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 9911) covalent geometry : angle 0.65544 / 0.31 (13474) hydrogen bonds : bond 0.05264 / 3.46 ( 483) hydrogen bonds : angle 4.07181 / 2.88 ( 1443) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8726 (t0) cc_final: 0.8315 (m-40) REVERT: A 26 LYS cc_start: 0.8580 (tttm) cc_final: 0.8136 (mmtp) REVERT: A 80 GLU cc_start: 0.7830 (tp30) cc_final: 0.7197 (mm-30) REVERT: A 139 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 215 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6571 (mtt) REVERT: B 31 LYS cc_start: 0.7994 (mptt) cc_final: 0.7281 (mttt) REVERT: B 80 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: B 153 ASP cc_start: 0.7888 (t70) cc_final: 0.7599 (t0) REVERT: C 14 GLN cc_start: 0.7566 (mt0) cc_final: 0.7224 (mp10) REVERT: C 80 GLU cc_start: 0.7958 (tp30) cc_final: 0.7564 (tp30) REVERT: C 125 ILE cc_start: 0.8467 (mm) cc_final: 0.8242 (mm) REVERT: C 212 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6167 (tp) REVERT: D 31 LYS cc_start: 0.7776 (tppp) cc_final: 0.7179 (mttt) REVERT: D 198 ASP cc_start: 0.7841 (t0) cc_final: 0.7631 (t0) REVERT: E 11 MET cc_start: 0.6342 (tmm) cc_final: 0.6131 (ppp) REVERT: E 31 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7422 (mttt) REVERT: E 141 LYS cc_start: 0.8204 (tttm) cc_final: 0.7954 (ttmm) REVERT: E 142 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7448 (mt) REVERT: E 177 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5365 (tp40) REVERT: F 31 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7737 (mttt) REVERT: F 80 GLU cc_start: 0.7438 (tp30) cc_final: 0.7008 (mm-30) REVERT: F 113 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6839 (mp10) outliers start: 54 outliers final: 39 residues processed: 233 average time/residue: 0.1063 time to fit residues: 33.6389 Evaluate side-chains 233 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137679 restraints weight = 11877.542| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.86 r_work: 0.3289 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 0.75 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 0.73 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (17 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9912 Z= 0.109 Angle : 0.588 10.899 13474 Z= 0.277 Chirality : 0.042 0.353 1524 Planarity : 0.004 0.032 1728 Dihedral : 12.155 84.276 1398 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.60 % Allowed : 20.93 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.39 (0.25), residues: 1212 helix: 0.31 (0.20), residues: 762 sheet: None (None), residues: 0 loop : 0.46 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 144 TYR 0.005 0.001 TYR E 131 PHE 0.007 0.001 PHE E 33 TRP 0.026 0.001 TRP E 185 HIS 0.004 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9911) covalent geometry : angle 0.58810 / 0.28 (13474) hydrogen bonds : bond 0.03573 / 2.37 ( 483) hydrogen bonds : angle 3.88088 / 2.75 ( 1443) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8498 (t0) cc_final: 0.8118 (m110) REVERT: A 26 LYS cc_start: 0.8605 (tttm) cc_final: 0.8189 (mmtp) REVERT: A 80 GLU cc_start: 0.7954 (tp30) cc_final: 0.7198 (mm-30) REVERT: A 153 ASP cc_start: 0.8063 (t70) cc_final: 0.7848 (t0) REVERT: A 215 MET cc_start: 0.7037 (mpp) cc_final: 0.6713 (mtt) REVERT: B 31 LYS cc_start: 0.7844 (mptt) cc_final: 0.7241 (mttt) REVERT: B 80 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 142 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7476 (mt) REVERT: B 153 ASP cc_start: 0.8049 (t70) cc_final: 0.7819 (t0) REVERT: C 14 GLN cc_start: 0.7369 (mt0) cc_final: 0.7139 (mp10) REVERT: C 80 GLU cc_start: 0.7920 (tp30) cc_final: 0.7502 (tp30) REVERT: C 139 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8483 (mt) REVERT: C 185 TRP cc_start: 0.6233 (t60) cc_final: 0.5527 (t60) REVERT: D 31 LYS cc_start: 0.7510 (tppp) cc_final: 0.6883 (mttt) REVERT: D 67 MET cc_start: 0.8367 (mmm) cc_final: 0.8078 (mmt) REVERT: D 203 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7261 (mm) REVERT: E 11 MET cc_start: 0.6418 (tmm) cc_final: 0.6023 (ptm) REVERT: E 31 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7389 (mttt) REVERT: E 141 LYS cc_start: 0.8164 (tttm) cc_final: 0.7883 (ttmm) REVERT: E 142 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7600 (mt) REVERT: E 177 GLN cc_start: 0.5874 (OUTLIER) cc_final: 0.5110 (tp40) REVERT: E 198 ASP cc_start: 0.7716 (t0) cc_final: 0.7414 (t0) REVERT: F 22 ASN cc_start: 0.8815 (t0) cc_final: 0.8508 (m-40) REVERT: F 113 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6923 (mp10) REVERT: F 139 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8144 (mt) outliers start: 38 outliers final: 25 residues processed: 218 average time/residue: 0.1162 time to fit residues: 33.7777 Evaluate side-chains 216 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.169929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131864 restraints weight = 12112.027| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.87 r_work: 0.3247 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 0.73 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 0.70 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 15 (21 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9912 Z= 0.164 Angle : 0.657 10.748 13474 Z= 0.312 Chirality : 0.044 0.289 1524 Planarity : 0.004 0.033 1728 Dihedral : 11.683 76.831 1397 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.40 % Allowed : 20.45 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.06 (0.24), residues: 1212 helix: 0.08 (0.20), residues: 744 sheet: -1.08 (0.63), residues: 66 loop : 0.27 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 144 TYR 0.008 0.001 TYR A 170 PHE 0.011 0.002 PHE D 169 TRP 0.031 0.002 TRP E 185 HIS 0.005 0.001 HIS C 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 9911) covalent geometry : angle 0.65745 / 0.31 (13474) hydrogen bonds : bond 0.04953 / 3.24 ( 483) hydrogen bonds : angle 3.99384 / 2.83 ( 1443) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8685 (t0) cc_final: 0.8290 (m-40) REVERT: A 26 LYS cc_start: 0.8568 (tttm) cc_final: 0.8164 (mmtp) REVERT: A 80 GLU cc_start: 0.7876 (tp30) cc_final: 0.7144 (mm-30) REVERT: A 137 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 139 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8370 (mt) REVERT: A 215 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: B 31 LYS cc_start: 0.7876 (mptt) cc_final: 0.7275 (mttt) REVERT: B 80 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: B 153 ASP cc_start: 0.7985 (t70) cc_final: 0.7736 (t0) REVERT: C 1 MET cc_start: 0.2690 (tmm) cc_final: 0.2093 (tpp) REVERT: C 80 GLU cc_start: 0.7969 (tp30) cc_final: 0.7617 (tp30) REVERT: C 185 TRP cc_start: 0.6325 (t60) cc_final: 0.5648 (t60) REVERT: C 212 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6188 (tp) REVERT: D 31 LYS cc_start: 0.7673 (tppp) cc_final: 0.7144 (mttt) REVERT: E 11 MET cc_start: 0.6353 (tmm) cc_final: 0.5985 (ptm) REVERT: E 31 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7424 (mttt) REVERT: E 141 LYS cc_start: 0.8167 (tttm) cc_final: 0.7902 (ttmm) REVERT: E 142 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7575 (mt) REVERT: E 177 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5391 (tp40) REVERT: F 80 GLU cc_start: 0.7584 (tp30) cc_final: 0.7320 (mm-30) REVERT: F 113 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7051 (mp10) outliers start: 57 outliers final: 41 residues processed: 231 average time/residue: 0.1107 time to fit residues: 34.4291 Evaluate side-chains 231 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN B 220 GLN ** D 180 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 = 0.3781 r_free = 0.3781 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126574 restraints weight = 12019.013| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3259 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 0.70 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 0.67 min = 0.05 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9912 Z= 0.176 Angle : 0.673 10.642 13474 Z= 0.323 Chirality : 0.045 0.211 1524 Planarity : 0.004 0.036 1728 Dihedral : 11.221 71.989 1397 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.53 % Allowed : 20.45 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.23 (0.24), residues: 1212 helix: -0.02 (0.19), residues: 744 sheet: -1.17 (0.61), residues: 66 loop : 0.15 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 163 TYR 0.006 0.001 TYR E 165 PHE 0.010 0.002 PHE D 169 TRP 0.034 0.002 TRP E 185 HIS 0.005 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 9911) covalent geometry : angle 0.67273 / 0.32 (13474) hydrogen bonds : bond 0.05051 / 3.31 ( 483) hydrogen bonds : angle 4.03705 / 2.86 ( 1443) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 183 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5689 (ppp) REVERT: A 13 HIS cc_start: 0.4982 (OUTLIER) cc_final: 0.4677 (p-80) REVERT: A 22 ASN cc_start: 0.8814 (t0) cc_final: 0.8376 (m-40) REVERT: A 26 LYS cc_start: 0.8607 (tttm) cc_final: 0.8105 (mmtp) REVERT: A 80 GLU cc_start: 0.7764 (tp30) cc_final: 0.7042 (mm-30) REVERT: A 137 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 139 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8386 (mt) REVERT: A 215 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6880 (mtt) REVERT: B 31 LYS cc_start: 0.7904 (mptt) cc_final: 0.7255 (mttt) REVERT: B 80 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: B 153 ASP cc_start: 0.8168 (t70) cc_final: 0.7897 (t0) REVERT: B 186 MET cc_start: 0.8356 (mtt) cc_final: 0.7772 (mtt) REVERT: C 1 MET cc_start: 0.2557 (tmm) cc_final: 0.2061 (tpp) REVERT: C 80 GLU cc_start: 0.7917 (tp30) cc_final: 0.7493 (tp30) REVERT: C 212 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6265 (tp) REVERT: D 31 LYS cc_start: 0.7657 (tppp) cc_final: 0.7108 (mttt) REVERT: E 11 MET cc_start: 0.6341 (tmm) cc_final: 0.6053 (ptm) REVERT: E 31 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7414 (mttt) REVERT: E 141 LYS cc_start: 0.8193 (tttm) cc_final: 0.7932 (ttmm) REVERT: E 142 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7572 (mt) REVERT: F 80 GLU cc_start: 0.7633 (tp30) cc_final: 0.7259 (mm-30) REVERT: F 113 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7106 (mp10) outliers start: 69 outliers final: 50 residues processed: 238 average time/residue: 0.1055 time to fit residues: 34.0137 Evaluate side-chains 238 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.0040 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135735 restraints weight = 11979.417| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.58 r_work: 0.3300 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 0.67 min = 0.05 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 0.66 min = 0.05 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9912 Z= 0.114 Angle : 0.603 10.178 13474 Z= 0.287 Chirality : 0.041 0.197 1524 Planarity : 0.004 0.035 1728 Dihedral : 10.316 68.212 1397 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.26 % Allowed : 22.54 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.18 (0.25), residues: 1212 helix: 0.29 (0.20), residues: 756 sheet: -1.10 (0.62), residues: 66 loop : 0.37 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 144 TYR 0.005 0.001 TYR E 131 PHE 0.007 0.001 PHE B 33 TRP 0.038 0.001 TRP E 185 HIS 0.004 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9911) covalent geometry : angle 0.60298 / 0.29 (13474) hydrogen bonds : bond 0.03577 / 2.36 ( 483) hydrogen bonds : angle 3.83913 / 2.72 ( 1443) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.240 Fit side-chains REVERT: A 11 MET cc_start: 0.6106 (tmm) cc_final: 0.5578 (ppp) REVERT: A 22 ASN cc_start: 0.8633 (t0) cc_final: 0.8260 (m110) REVERT: A 26 LYS cc_start: 0.8680 (tttm) cc_final: 0.8186 (mmtp) REVERT: A 80 GLU cc_start: 0.7829 (tp30) cc_final: 0.7194 (mm-30) REVERT: A 139 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 215 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: B 31 LYS cc_start: 0.7839 (mptt) cc_final: 0.7273 (mttt) REVERT: B 80 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 142 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 153 ASP cc_start: 0.8154 (t70) cc_final: 0.7912 (t0) REVERT: C 80 GLU cc_start: 0.7833 (tp30) cc_final: 0.7393 (tp30) REVERT: C 139 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8536 (mt) REVERT: C 185 TRP cc_start: 0.6312 (t60) cc_final: 0.5642 (t60) REVERT: C 212 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6308 (tp) REVERT: D 31 LYS cc_start: 0.7558 (tppp) cc_final: 0.6965 (mttt) REVERT: D 203 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7049 (mp) REVERT: E 11 MET cc_start: 0.6230 (tmm) cc_final: 0.5894 (ptm) REVERT: E 31 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7439 (mttt) REVERT: E 141 LYS cc_start: 0.8234 (tttm) cc_final: 0.7965 (ttmm) REVERT: E 142 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7707 (mt) REVERT: F 22 ASN cc_start: 0.8961 (t0) cc_final: 0.8647 (m-40) REVERT: F 113 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7190 (mp10) outliers start: 45 outliers final: 30 residues processed: 216 average time/residue: 0.1044 time to fit residues: 30.3833 Evaluate side-chains 218 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.162230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131388 restraints weight = 12024.363| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.56 r_work: 0.3269 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 0.66 min = 0.05 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 0.69 min = 0.06 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9912 Z= 0.162 Angle : 0.658 9.602 13474 Z= 0.317 Chirality : 0.043 0.215 1524 Planarity : 0.004 0.036 1728 Dihedral : 10.029 67.035 1394 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.92 % Allowed : 22.06 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.05 (0.24), residues: 1212 helix: 0.12 (0.19), residues: 756 sheet: -1.18 (0.60), residues: 66 loop : 0.23 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.007 0.001 TYR A 170 PHE 0.010 0.002 PHE D 169 TRP 0.033 0.002 TRP E 185 HIS 0.006 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 9911) covalent geometry : angle 0.65784 / 0.32 (13474) hydrogen bonds : bond 0.04779 / 3.12 ( 483) hydrogen bonds : angle 3.97138 / 2.83 ( 1443) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.311 Fit side-chains REVERT: A 11 MET cc_start: 0.6119 (tmm) cc_final: 0.5768 (ppp) REVERT: A 22 ASN cc_start: 0.8824 (t0) cc_final: 0.8526 (m110) REVERT: A 26 LYS cc_start: 0.8688 (tttm) cc_final: 0.8187 (mmtp) REVERT: A 80 GLU cc_start: 0.7804 (tp30) cc_final: 0.7133 (mm-30) REVERT: A 139 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 215 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6881 (mtt) REVERT: B 31 LYS cc_start: 0.7920 (mptt) cc_final: 0.7328 (mttt) REVERT: B 80 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: B 153 ASP cc_start: 0.8161 (t70) cc_final: 0.7922 (t0) REVERT: C 80 GLU cc_start: 0.7842 (tp30) cc_final: 0.7498 (tp30) REVERT: C 212 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.6052 (tp) REVERT: D 31 LYS cc_start: 0.7734 (tppp) cc_final: 0.7160 (mttt) REVERT: E 11 MET cc_start: 0.6272 (tmm) cc_final: 0.5891 (ptm) REVERT: E 31 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7493 (mttt) REVERT: E 141 LYS cc_start: 0.8244 (tttm) cc_final: 0.7987 (ttmm) REVERT: E 142 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7610 (mt) REVERT: F 113 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7280 (mp10) outliers start: 52 outliers final: 41 residues processed: 221 average time/residue: 0.1056 time to fit residues: 31.6817 Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131721 restraints weight = 11961.315| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.52 r_work: 0.3269 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 0.69 min = 0.06 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 0.66 min = 0.06 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 18 (25 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9912 Z= 0.154 Angle : 0.659 10.283 13474 Z= 0.319 Chirality : 0.043 0.229 1524 Planarity : 0.004 0.035 1728 Dihedral : 9.773 65.325 1394 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.55 % Allowed : 22.73 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.07 (0.24), residues: 1212 helix: 0.12 (0.19), residues: 756 sheet: -1.33 (0.59), residues: 66 loop : 0.23 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 155 TYR 0.005 0.001 TYR E 165 PHE 0.009 0.001 PHE B 33 TRP 0.031 0.001 TRP E 185 HIS 0.005 0.001 HIS F 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 9911) covalent geometry : angle 0.65906 / 0.32 (13474) hydrogen bonds : bond 0.04547 / 2.98 ( 483) hydrogen bonds : angle 3.98222 / 2.84 ( 1443) Misc. bond : bond 0.00062 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.368 Fit side-chains REVERT: A 11 MET cc_start: 0.6017 (tmm) cc_final: 0.5770 (ppp) REVERT: A 22 ASN cc_start: 0.8801 (t0) cc_final: 0.8469 (m-40) REVERT: A 26 LYS cc_start: 0.8683 (tttm) cc_final: 0.8175 (mmtp) REVERT: A 80 GLU cc_start: 0.7852 (tp30) cc_final: 0.7193 (mm-30) REVERT: A 139 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 215 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6907 (mtt) REVERT: B 31 LYS cc_start: 0.7899 (mptt) cc_final: 0.7271 (mttt) REVERT: B 80 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: B 153 ASP cc_start: 0.8166 (t70) cc_final: 0.7913 (t0) REVERT: C 80 GLU cc_start: 0.7805 (tp30) cc_final: 0.7449 (tp30) REVERT: C 212 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6175 (tp) REVERT: D 31 LYS cc_start: 0.7709 (tppp) cc_final: 0.7124 (mttt) REVERT: E 11 MET cc_start: 0.6310 (tmm) cc_final: 0.5889 (ptm) REVERT: E 31 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7471 (mttt) REVERT: E 112 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7804 (pt) REVERT: E 141 LYS cc_start: 0.8229 (tttm) cc_final: 0.7968 (ttmm) REVERT: E 142 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7638 (mt) REVERT: F 113 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7310 (mp10) REVERT: F 189 THR cc_start: 0.4966 (m) cc_final: 0.4427 (p) outliers start: 48 outliers final: 38 residues processed: 221 average time/residue: 0.1045 time to fit residues: 31.3589 Evaluate side-chains 221 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 70 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135500 restraints weight = 11884.404| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.48 r_work: 0.3310 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 0.66 min = 0.06 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 0.51 min = 0.03 number of occupancies < 0.1: 289 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 26 (32 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9912 Z= 0.120 Angle : 0.617 9.598 13474 Z= 0.300 Chirality : 0.041 0.228 1524 Planarity : 0.004 0.044 1728 Dihedral : 9.346 62.224 1394 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.36 % Allowed : 22.92 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.33 (0.25), residues: 1212 helix: 0.41 (0.20), residues: 756 sheet: -1.25 (0.62), residues: 66 loop : 0.44 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.005 0.001 TYR E 131 PHE 0.007 0.001 PHE E 33 TRP 0.031 0.001 TRP E 185 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9911) covalent geometry : angle 0.61713 / 0.30 (13474) hydrogen bonds : bond 0.03590 / 2.36 ( 483) hydrogen bonds : angle 3.85403 / 2.74 ( 1443) Misc. bond : bond 0.00041 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.21 seconds wall clock time: 38 minutes 0.26 seconds (2280.26 seconds total)