Starting phenix.real_space_refine on Sun Aug 9 17:31:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.map" model { file = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2026/8ane_15540.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 66 5.49 5 S 56 5.16 5 C 11536 2.51 5 N 3263 2.21 5 O 3624 1.98 5 H 18195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 36740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 295} Chain: "B" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "D" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "E" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "F" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "G" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4948 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "R" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 2104 Classifications: {'RNAv2': 66} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 18, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 26, 'rna3p': 39} Time building chain proxies: 5.10, per 1000 atoms: 0.14 Number of scatterers: 36740 At special positions: 0 Unit cell: (117.936, 156.24, 168.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 66 15.00 O 3624 8.00 N 3263 7.00 C 11536 6.00 H 18195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 906.1 milliseconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 36 sheets defined 36.5% alpha, 20.1% beta 2 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.667A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.523A pdb=" N GLU A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 4.007A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 164 removed outlier: 5.816A pdb=" N GLY A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 163 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.960A pdb=" N ALA A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 53 through 65 removed outlier: 3.688A pdb=" N ASN B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.866A pdb=" N ASP B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.522A pdb=" N VAL B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.540A pdb=" N VAL B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.957A pdb=" N ILE B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 257 removed outlier: 3.963A pdb=" N VAL B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 301 removed outlier: 3.524A pdb=" N ALA B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.568A pdb=" N THR C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.828A pdb=" N ASP C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 removed outlier: 3.708A pdb=" N GLU C 128 " --> pdb=" O ALA C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.513A pdb=" N VAL C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.508A pdb=" N ARG C 164 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.855A pdb=" N GLY C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 257 Processing helix chain 'C' and resid 283 through 301 Proline residue: C 292 - end of helix Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.573A pdb=" N ASP D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 4.256A pdb=" N CYS D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 114 through 125 removed outlier: 4.373A pdb=" N ASP D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.581A pdb=" N HIS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.672A pdb=" N ILE D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 254 Processing helix chain 'D' and resid 283 through 301 Proline residue: D 292 - end of helix Processing helix chain 'E' and resid 3 through 10 removed outlier: 3.551A pdb=" N LEU E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 75 through 78 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 114 through 128 removed outlier: 5.164A pdb=" N GLU E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N HIS E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 145 through 152 removed outlier: 4.051A pdb=" N VAL E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 150 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 236 through 254 Processing helix chain 'E' and resid 283 through 301 Proline residue: E 292 - end of helix Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.516A pdb=" N SER F 8 " --> pdb=" O PRO F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.763A pdb=" N ASP F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 133 through 145 removed outlier: 3.771A pdb=" N VAL F 144 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 198 through 202 removed outlier: 3.768A pdb=" N ARG F 201 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.546A pdb=" N GLY F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 257 Processing helix chain 'F' and resid 283 through 301 Proline residue: F 292 - end of helix Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 53 through 64 removed outlier: 3.782A pdb=" N GLU G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'G' and resid 117 through 129 removed outlier: 3.759A pdb=" N HIS G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 145 removed outlier: 3.518A pdb=" N LEU G 137 " --> pdb=" O ASP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 152 removed outlier: 3.731A pdb=" N VAL G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 Processing helix chain 'G' and resid 225 through 233 Processing helix chain 'G' and resid 235 through 257 removed outlier: 4.116A pdb=" N VAL G 255 " --> pdb=" O ARG G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 301 Proline residue: G 292 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 6.431A pdb=" N ILE A 175 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A 217 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 218 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 270 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 20 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N CYS A 268 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.622A pdb=" N ASP A 72 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.132A pdb=" N THR A 94 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 310 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 188 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 41 removed outlier: 4.740A pdb=" N ALA B 38 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 175 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG B 217 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 218 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 14 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 270 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 20 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS B 268 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 189 removed outlier: 3.622A pdb=" N VAL B 206 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.601A pdb=" N ALA C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 178 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 217 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE C 218 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 14 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 270 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 20 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N CYS C 268 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB6, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 189 removed outlier: 3.742A pdb=" N VAL C 206 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.630A pdb=" N ILE D 175 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG D 217 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 218 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 14 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP D 18 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 270 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 20 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS D 268 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.638A pdb=" N VAL D 82 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 312 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 84 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 189 Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 41 removed outlier: 7.137A pdb=" N ILE E 175 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG E 217 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE E 218 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 14 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 270 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 20 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS E 268 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 261 " --> pdb=" O CYS E 264 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E 266 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG E 259 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC6, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AC7, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AC8, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'E' and resid 187 through 188 Processing sheet with id=AD1, first strand: chain 'F' and resid 39 through 41 removed outlier: 7.158A pdb=" N ILE F 175 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG F 217 " --> pdb=" O GLU F 178 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE F 218 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 14 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL F 273 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU F 16 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 271 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP F 18 " --> pdb=" O GLN F 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 92 through 95 removed outlier: 3.517A pdb=" N THR F 94 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD4, first strand: chain 'F' and resid 181 through 188 Processing sheet with id=AD5, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.636A pdb=" N ILE G 175 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 178 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG G 217 " --> pdb=" O GLU G 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE G 218 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU G 14 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA G 270 " --> pdb=" O ASP G 18 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL G 20 " --> pdb=" O CYS G 268 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N CYS G 268 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU G 266 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 259 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 26 through 27 removed outlier: 3.600A pdb=" N PHE G 27 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR G 213 " --> pdb=" O PHE G 27 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.693A pdb=" N ASP G 72 " --> pdb=" O ASP G 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AD9, first strand: chain 'G' and resid 153 through 154 720 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 5982 1.05 - 1.24: 14392 1.24 - 1.43: 5683 1.43 - 1.62: 11088 1.62 - 1.81: 91 Bond restraints: 37236 Sorted by residual: bond pdb=" NE1 TRP C 279 " pdb=" HE1 TRP C 279 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP F 66 " pdb=" HE1 TRP F 66 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP F 73 " pdb=" HE1 TRP F 73 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP G 279 " pdb=" HE1 TRP G 279 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 66 " pdb=" HE1 TRP D 66 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 37231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 61546 2.15 - 4.30: 5475 4.30 - 6.45: 585 6.45 - 8.60: 84 8.60 - 10.74: 6 Bond angle restraints: 67696 Sorted by residual: angle pdb=" N TYR B 40 " pdb=" CA TYR B 40 " pdb=" C TYR B 40 " ideal model delta sigma weight residual 107.88 115.12 -7.24 1.41e+00 5.03e-01 2.64e+01 angle pdb=" N THR B 140 " pdb=" CA THR B 140 " pdb=" C THR B 140 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 angle pdb=" C3' A R 10 " pdb=" O3' A R 10 " pdb=" P G R 11 " ideal model delta sigma weight residual 119.70 124.36 -4.66 1.20e+00 6.94e-01 1.51e+01 angle pdb=" C3' G R 42 " pdb=" O3' G R 42 " pdb=" P G R 43 " ideal model delta sigma weight residual 119.70 124.31 -4.61 1.20e+00 6.94e-01 1.47e+01 angle pdb=" O3' G R 38 " pdb=" C3' G R 38 " pdb=" H3' G R 38 " ideal model delta sigma weight residual 109.00 98.26 10.74 3.00e+00 1.11e-01 1.28e+01 ... (remaining 67691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 16454 35.71 - 71.42: 669 71.42 - 107.14: 37 107.14 - 142.85: 0 142.85 - 178.56: 5 Dihedral angle restraints: 17165 sinusoidal: 10025 harmonic: 7140 Sorted by residual: dihedral pdb=" C4' C R 53 " pdb=" C3' C R 53 " pdb=" C2' C R 53 " pdb=" C1' C R 53 " ideal model delta sinusoidal sigma weight residual 36.34 -39.66 76.01 1 3.10e+00 1.04e-01 7.57e+02 dihedral pdb=" C4' C R 26 " pdb=" C3' C R 26 " pdb=" C2' C R 26 " pdb=" C1' C R 26 " ideal model delta sinusoidal sigma weight residual 36.34 -39.16 75.50 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' U R 59 " pdb=" C3' U R 59 " pdb=" C2' U R 59 " pdb=" C1' U R 59 " ideal model delta sinusoidal sigma weight residual 36.34 -38.77 75.11 1 3.10e+00 1.04e-01 7.42e+02 ... (remaining 17162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2560 0.065 - 0.130: 323 0.130 - 0.194: 39 0.194 - 0.259: 80 0.259 - 0.324: 30 Chirality restraints: 3032 Sorted by residual: chirality pdb=" P G R 43 " pdb=" OP1 G R 43 " pdb=" OP2 G R 43 " pdb=" O5' G R 43 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" P G R 45 " pdb=" OP1 G R 45 " pdb=" OP2 G R 45 " pdb=" O5' G R 45 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" P G R 11 " pdb=" OP1 G R 11 " pdb=" OP2 G R 11 " pdb=" O5' G R 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3029 not shown) Planarity restraints: 5295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 136 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C LYS F 136 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS F 136 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 137 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 41 " -0.031 2.00e-02 2.50e+03 1.49e-02 6.66e+00 pdb=" N1 U R 41 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U R 41 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U R 41 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U R 41 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U R 41 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U R 41 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U R 41 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U R 41 " 0.008 2.00e-02 2.50e+03 pdb=" H5 U R 41 " 0.002 2.00e-02 2.50e+03 pdb=" H3 U R 41 " -0.013 2.00e-02 2.50e+03 pdb=" H6 U R 41 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 292 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C PRO F 292 " -0.042 2.00e-02 2.50e+03 pdb=" O PRO F 292 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY F 293 " 0.014 2.00e-02 2.50e+03 ... (remaining 5292 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 969 2.05 - 2.69: 52385 2.69 - 3.33: 104952 3.33 - 3.96: 136853 3.96 - 4.60: 207960 Nonbonded interactions: 503119 Sorted by model distance: nonbonded pdb=" HG1 THR E 25 " pdb=" HH TYR F 40 " model vdw 1.419 2.100 nonbonded pdb=" O2 C R 40 " pdb="HO2' C R 40 " model vdw 1.487 2.450 nonbonded pdb="HO2' U R 59 " pdb=" H61 A R 61 " model vdw 1.504 2.100 nonbonded pdb="HD13 LEU E 150 " pdb=" HZ2 LYS E 249 " model vdw 1.542 2.270 nonbonded pdb=" O2 U R 46 " pdb="HO2' U R 46 " model vdw 1.549 2.450 ... (remaining 503114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 35.920 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 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 : 0.003 0.070 19041 Z= 0.144 Angle : 0.725 7.281 26142 Z= 0.350 Chirality : 0.063 0.324 3032 Planarity : 0.006 0.066 3181 Dihedral : 16.867 178.561 7397 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.93 % Allowed : 8.85 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2198 helix: -1.60 (0.17), residues: 675 sheet: 0.71 (0.25), residues: 414 loop : -1.88 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.010 0.001 TYR B 40 PHE 0.019 0.001 PHE G 208 TRP 0.015 0.001 TRP D 279 HIS 0.006 0.001 HIS G 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (19041) covalent geometry : angle 0.72509 / 0.35 (26142) hydrogen bonds : bond 0.16549 / 10.93 ( 726) hydrogen bonds : angle 7.78717 / 5.40 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 419 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.1906 (mtmt) cc_final: 0.1381 (mttp) REVERT: B 262 THR cc_start: 0.5108 (t) cc_final: 0.4766 (t) REVERT: C 41 GLU cc_start: 0.5582 (mp0) cc_final: 0.4218 (tt0) REVERT: D 25 THR cc_start: 0.6299 (p) cc_final: 0.6003 (p) REVERT: D 181 ARG cc_start: 0.7008 (mpt-90) cc_final: 0.6599 (mpt180) REVERT: E 1 MET cc_start: 0.1721 (mmm) cc_final: -0.0072 (mpp) REVERT: E 51 VAL cc_start: 0.4340 (t) cc_final: 0.3858 (t) REVERT: E 116 LEU cc_start: 0.7126 (tp) cc_final: 0.6904 (tt) REVERT: F 117 PHE cc_start: 0.5680 (t80) cc_final: 0.5114 (t80) REVERT: F 261 ARG cc_start: 0.4407 (ttm110) cc_final: 0.3507 (mtm-85) REVERT: F 314 TYR cc_start: 0.3125 (t80) cc_final: 0.2322 (t80) REVERT: G 159 GLU cc_start: 0.5774 (mp0) cc_final: 0.5569 (mt-10) REVERT: G 269 GLN cc_start: 0.3818 (mt0) cc_final: 0.3202 (tm-30) outliers start: 17 outliers final: 7 residues processed: 429 average time/residue: 0.3590 time to fit residues: 219.8083 Evaluate side-chains 252 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 245 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 303 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN B 59 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.241208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.211267 restraints weight = 86238.232| |-----------------------------------------------------------------------------| r_work (start): 0.4982 rms_B_bonded: 2.54 r_work: 0.4825 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5237 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19041 Z= 0.238 Angle : 1.192 22.856 26142 Z= 0.492 Chirality : 0.075 0.733 3032 Planarity : 0.006 0.082 3181 Dihedral : 16.967 179.459 3214 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.31 % Allowed : 12.91 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2198 helix: -0.39 (0.19), residues: 687 sheet: 0.38 (0.24), residues: 425 loop : -1.88 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 272 TYR 0.013 0.002 TYR D 221 PHE 0.014 0.002 PHE G 208 TRP 0.009 0.001 TRP G 66 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (19041) covalent geometry : angle 1.19173 / 0.49 (26142) hydrogen bonds : bond 0.04720 / 3.11 ( 726) hydrogen bonds : angle 6.12012 / 4.25 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLN cc_start: 0.2833 (mp10) cc_final: 0.2526 (mp10) REVERT: B 48 MET cc_start: 0.4647 (mmt) cc_final: 0.3959 (ptt) REVERT: B 258 LEU cc_start: 0.6228 (mt) cc_final: 0.6014 (mt) REVERT: C 23 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.5819 (mm110) REVERT: E 1 MET cc_start: 0.1867 (mmm) cc_final: 0.0323 (mpp) REVERT: E 116 LEU cc_start: 0.7429 (tp) cc_final: 0.7210 (tt) REVERT: F 74 VAL cc_start: 0.3229 (m) cc_final: 0.1683 (t) REVERT: F 109 LEU cc_start: 0.5702 (tp) cc_final: 0.5404 (tp) REVERT: F 229 ILE cc_start: 0.6311 (pt) cc_final: 0.6101 (pt) REVERT: F 314 TYR cc_start: 0.3634 (t80) cc_final: 0.2834 (t80) REVERT: G 159 GLU cc_start: 0.6042 (mp0) cc_final: 0.5731 (mt-10) REVERT: G 269 GLN cc_start: 0.3909 (mt0) cc_final: 0.3286 (tm-30) outliers start: 42 outliers final: 25 residues processed: 307 average time/residue: 0.3118 time to fit residues: 143.0134 Evaluate side-chains 240 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 170 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN C 147 ASN C 256 HIS F 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.225164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.191362 restraints weight = 83205.182| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 2.74 r_work: 0.4657 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 19041 Z= 0.190 Angle : 0.889 13.937 26142 Z= 0.395 Chirality : 0.058 0.435 3032 Planarity : 0.006 0.064 3181 Dihedral : 16.802 178.703 3209 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.14 % Allowed : 14.67 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2198 helix: 0.03 (0.20), residues: 658 sheet: 0.03 (0.24), residues: 431 loop : -1.84 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 303 TYR 0.053 0.002 TYR A 213 PHE 0.014 0.002 PHE G 32 TRP 0.011 0.002 TRP B 66 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (19041) covalent geometry : angle 0.88898 / 0.39 (26142) hydrogen bonds : bond 0.04553 / 3.00 ( 726) hydrogen bonds : angle 5.83426 / 4.06 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.1657 (mtmt) cc_final: 0.1284 (ptpp) REVERT: B 18 ASP cc_start: 0.5109 (p0) cc_final: 0.4856 (p0) REVERT: B 48 MET cc_start: 0.4546 (mmt) cc_final: 0.3788 (ptt) REVERT: C 23 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.5686 (mm110) REVERT: E 1 MET cc_start: 0.2155 (mmm) cc_final: 0.0457 (mpp) REVERT: E 117 PHE cc_start: 0.7472 (t80) cc_final: 0.7232 (t80) REVERT: G 135 ARG cc_start: 0.5018 (mtt-85) cc_final: 0.4690 (mtm180) REVERT: G 159 GLU cc_start: 0.6039 (mp0) cc_final: 0.5754 (mt-10) outliers start: 39 outliers final: 30 residues processed: 264 average time/residue: 0.3041 time to fit residues: 121.6467 Evaluate side-chains 224 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 291 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 204 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 23 GLN C 269 GLN ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.208176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.174486 restraints weight = 80486.467| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 2.23 r_work: 0.4495 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4386 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 19041 Z= 0.206 Angle : 0.948 17.196 26142 Z= 0.425 Chirality : 0.060 0.612 3032 Planarity : 0.007 0.084 3181 Dihedral : 16.383 176.747 3207 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.80 % Allowed : 16.98 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2198 helix: -0.11 (0.20), residues: 664 sheet: -0.46 (0.24), residues: 467 loop : -1.86 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 272 TYR 0.019 0.002 TYR E 248 PHE 0.017 0.002 PHE A 27 TRP 0.019 0.002 TRP G 73 HIS 0.008 0.002 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (19041) covalent geometry : angle 0.94813 / 0.43 (26142) hydrogen bonds : bond 0.04341 / 2.84 ( 726) hydrogen bonds : angle 5.63676 / 3.90 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.4540 (mmt) cc_final: 0.3990 (ptt) REVERT: B 69 ASP cc_start: 0.6257 (t70) cc_final: 0.5939 (m-30) REVERT: B 210 ARG cc_start: 0.6407 (mtp180) cc_final: 0.6155 (mtm-85) REVERT: B 309 VAL cc_start: 0.6581 (t) cc_final: 0.6088 (p) REVERT: C 23 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6411 (mt0) REVERT: C 298 VAL cc_start: 0.5066 (t) cc_final: 0.4720 (p) REVERT: C 311 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7978 (mt) REVERT: D 69 ASP cc_start: 0.6962 (p0) cc_final: 0.6740 (p0) REVERT: E 1 MET cc_start: 0.2231 (mmm) cc_final: 0.0214 (mpp) REVERT: E 117 PHE cc_start: 0.7533 (t80) cc_final: 0.7240 (t80) REVERT: F 169 ARG cc_start: 0.6475 (mtt90) cc_final: 0.6135 (mtp180) REVERT: F 181 ARG cc_start: 0.5153 (mpp80) cc_final: 0.4727 (mtt-85) REVERT: F 261 ARG cc_start: 0.5874 (ttm110) cc_final: 0.5517 (mtm-85) REVERT: G 68 LYS cc_start: 0.6858 (pttt) cc_final: 0.6050 (mmmt) REVERT: G 85 VAL cc_start: 0.6418 (t) cc_final: 0.5998 (m) REVERT: G 135 ARG cc_start: 0.5322 (mtt-85) cc_final: 0.4899 (mtm180) outliers start: 51 outliers final: 30 residues processed: 269 average time/residue: 0.3163 time to fit residues: 126.3257 Evaluate side-chains 213 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 137 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN B 59 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.199066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.164698 restraints weight = 79525.881| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 2.33 r_work: 0.4324 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19041 Z= 0.197 Angle : 0.854 12.895 26142 Z= 0.394 Chirality : 0.056 0.383 3032 Planarity : 0.006 0.097 3181 Dihedral : 16.535 177.800 3207 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.97 % Allowed : 17.20 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.17), residues: 2198 helix: -0.18 (0.21), residues: 648 sheet: -0.49 (0.24), residues: 466 loop : -1.95 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 272 TYR 0.010 0.002 TYR F 248 PHE 0.017 0.002 PHE F 32 TRP 0.013 0.002 TRP D 279 HIS 0.015 0.002 HIS F 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (19041) covalent geometry : angle 0.85357 / 0.39 (26142) hydrogen bonds : bond 0.04356 / 2.89 ( 726) hydrogen bonds : angle 5.68513 / 3.96 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.5023 (t80) cc_final: 0.4435 (t80) REVERT: B 48 MET cc_start: 0.4707 (mmt) cc_final: 0.4057 (ptt) REVERT: B 60 ARG cc_start: 0.6836 (mtt-85) cc_final: 0.6106 (mmt90) REVERT: B 69 ASP cc_start: 0.6110 (t70) cc_final: 0.5745 (m-30) REVERT: B 104 ASN cc_start: 0.5390 (OUTLIER) cc_final: 0.5023 (t0) REVERT: C 23 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.4990 (mt0) REVERT: C 105 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.7050 (m) REVERT: E 1 MET cc_start: 0.1865 (mmm) cc_final: -0.0221 (mpp) REVERT: E 117 PHE cc_start: 0.7380 (t80) cc_final: 0.7084 (t80) REVERT: F 109 LEU cc_start: 0.6052 (tp) cc_final: 0.5828 (tp) REVERT: F 169 ARG cc_start: 0.6960 (mtt90) cc_final: 0.6493 (mtp180) REVERT: F 181 ARG cc_start: 0.5368 (mpp80) cc_final: 0.4658 (mtt-85) REVERT: F 261 ARG cc_start: 0.5932 (ttm110) cc_final: 0.5438 (mtm-85) REVERT: G 48 MET cc_start: 0.5526 (mtt) cc_final: 0.5306 (mmt) REVERT: G 68 LYS cc_start: 0.6842 (pttt) cc_final: 0.5952 (mmmt) REVERT: G 85 VAL cc_start: 0.6538 (t) cc_final: 0.6061 (m) REVERT: G 135 ARG cc_start: 0.5535 (mtt-85) cc_final: 0.5027 (mtm180) outliers start: 54 outliers final: 37 residues processed: 249 average time/residue: 0.3053 time to fit residues: 114.8713 Evaluate side-chains 220 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 220 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN C 95 ASN D 190 ASN D 205 ASN G 59 ASN ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.186767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.152877 restraints weight = 79922.677| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.41 r_work: 0.4166 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.9900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19041 Z= 0.266 Angle : 1.006 16.740 26142 Z= 0.470 Chirality : 0.064 0.639 3032 Planarity : 0.008 0.130 3181 Dihedral : 16.530 177.111 3203 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.01 % Allowed : 17.69 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.17), residues: 2198 helix: -0.85 (0.20), residues: 657 sheet: -0.90 (0.24), residues: 488 loop : -2.28 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.002 ARG F 303 TYR 0.019 0.003 TYR B 40 PHE 0.026 0.003 PHE E 208 TRP 0.016 0.003 TRP C 73 HIS 0.016 0.003 HIS E 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (19041) covalent geometry : angle 1.00563 / 0.47 (26142) hydrogen bonds : bond 0.05047 / 3.35 ( 726) hydrogen bonds : angle 6.00991 / 4.17 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 203 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.5115 (t80) cc_final: 0.4874 (t80) REVERT: B 48 MET cc_start: 0.5015 (mmm) cc_final: 0.4318 (ptt) REVERT: B 60 ARG cc_start: 0.7207 (mtt-85) cc_final: 0.6878 (mmt90) REVERT: C 23 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.5013 (mt0) REVERT: D 83 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7581 (p) REVERT: D 127 MET cc_start: 0.6010 (tpp) cc_final: 0.5458 (mmp) REVERT: E 1 MET cc_start: 0.1309 (mmm) cc_final: -0.0456 (mmt) REVERT: F 212 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6076 (mt-10) REVERT: F 261 ARG cc_start: 0.6147 (ttm110) cc_final: 0.5782 (mtm-85) REVERT: G 68 LYS cc_start: 0.6843 (pttt) cc_final: 0.5942 (mmmt) REVERT: G 85 VAL cc_start: 0.6886 (t) cc_final: 0.6411 (m) REVERT: G 135 ARG cc_start: 0.5829 (mtt-85) cc_final: 0.5511 (mtm180) outliers start: 73 outliers final: 49 residues processed: 266 average time/residue: 0.3102 time to fit residues: 122.9359 Evaluate side-chains 217 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 279 TRP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.143677 restraints weight = 76134.446| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.88 r_work: 0.4150 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 1.0210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19041 Z= 0.151 Angle : 0.782 12.073 26142 Z= 0.361 Chirality : 0.054 0.492 3032 Planarity : 0.006 0.068 3181 Dihedral : 16.285 179.649 3203 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.47 % Allowed : 19.29 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2198 helix: -0.44 (0.20), residues: 663 sheet: -0.48 (0.25), residues: 462 loop : -2.08 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 303 TYR 0.016 0.001 TYR B 40 PHE 0.024 0.002 PHE F 232 TRP 0.014 0.001 TRP B 66 HIS 0.006 0.001 HIS F 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (19041) covalent geometry : angle 0.78170 / 0.36 (26142) hydrogen bonds : bond 0.04101 / 2.74 ( 726) hydrogen bonds : angle 5.59256 / 3.87 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.5043 (mmm) cc_final: 0.4399 (ptt) REVERT: B 60 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6418 (mtt180) REVERT: C 23 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.5128 (mt0) REVERT: E 1 MET cc_start: 0.1822 (mmm) cc_final: -0.0122 (mmt) REVERT: E 101 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.5082 (m170) REVERT: E 117 PHE cc_start: 0.7373 (t80) cc_final: 0.7094 (t80) REVERT: F 59 ASN cc_start: 0.6641 (m-40) cc_final: 0.6329 (m110) REVERT: F 261 ARG cc_start: 0.6000 (ttm110) cc_final: 0.5548 (mtm-85) REVERT: F 274 THR cc_start: 0.5449 (OUTLIER) cc_final: 0.5199 (m) REVERT: G 68 LYS cc_start: 0.6827 (pttt) cc_final: 0.5982 (mmmt) REVERT: G 85 VAL cc_start: 0.7029 (t) cc_final: 0.6665 (m) REVERT: G 135 ARG cc_start: 0.5936 (mtt-85) cc_final: 0.5570 (mtm180) outliers start: 45 outliers final: 35 residues processed: 221 average time/residue: 0.2991 time to fit residues: 100.5451 Evaluate side-chains 205 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 279 TRP Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 42 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.176941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.138122 restraints weight = 76614.499| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.94 r_work: 0.4077 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 1.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19041 Z= 0.199 Angle : 0.848 13.879 26142 Z= 0.397 Chirality : 0.056 0.554 3032 Planarity : 0.007 0.062 3181 Dihedral : 16.308 179.442 3203 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.91 % Allowed : 19.40 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2198 helix: -0.55 (0.20), residues: 657 sheet: -0.75 (0.24), residues: 490 loop : -2.16 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 303 TYR 0.031 0.002 TYR A 40 PHE 0.022 0.002 PHE F 32 TRP 0.015 0.002 TRP B 66 HIS 0.008 0.002 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (19041) covalent geometry : angle 0.84843 / 0.40 (26142) hydrogen bonds : bond 0.04457 / 2.98 ( 726) hydrogen bonds : angle 5.67465 / 3.94 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6207 (pm20) REVERT: B 60 ARG cc_start: 0.7009 (mtt-85) cc_final: 0.6780 (mmt90) REVERT: B 157 LYS cc_start: 0.5340 (ptpt) cc_final: 0.4394 (ptpp) REVERT: B 250 VAL cc_start: 0.7361 (OUTLIER) cc_final: 0.7022 (t) REVERT: C 23 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.5110 (mt0) REVERT: E 1 MET cc_start: 0.1559 (mmm) cc_final: -0.0172 (mmt) REVERT: F 212 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: F 274 THR cc_start: 0.5705 (OUTLIER) cc_final: 0.5445 (m) REVERT: G 48 MET cc_start: 0.6086 (mmt) cc_final: 0.5309 (mmt) REVERT: G 68 LYS cc_start: 0.6829 (pttt) cc_final: 0.6017 (mmmt) REVERT: G 85 VAL cc_start: 0.7342 (t) cc_final: 0.6985 (m) REVERT: G 135 ARG cc_start: 0.5953 (mtt-85) cc_final: 0.5723 (mtm180) REVERT: G 311 ILE cc_start: 0.6989 (mm) cc_final: 0.6752 (mm) outliers start: 53 outliers final: 42 residues processed: 225 average time/residue: 0.3037 time to fit residues: 104.2194 Evaluate side-chains 211 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 228 GLN Chi-restraints excluded: chain G residue 255 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 192 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.184345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.148980 restraints weight = 80474.206| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.59 r_work: 0.4135 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 1.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19041 Z= 0.138 Angle : 0.749 11.933 26142 Z= 0.345 Chirality : 0.052 0.511 3032 Planarity : 0.006 0.054 3181 Dihedral : 16.111 177.392 3201 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.36 % Allowed : 19.73 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 2198 helix: -0.22 (0.21), residues: 657 sheet: -0.45 (0.25), residues: 470 loop : -1.99 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 272 TYR 0.012 0.001 TYR B 40 PHE 0.021 0.001 PHE F 232 TRP 0.012 0.001 TRP B 66 HIS 0.007 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (19041) covalent geometry : angle 0.74869 / 0.35 (26142) hydrogen bonds : bond 0.03881 / 2.59 ( 726) hydrogen bonds : angle 5.37905 / 3.72 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: B 143 LYS cc_start: 0.3594 (OUTLIER) cc_final: 0.2948 (mmtt) REVERT: B 259 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5938 (ppt170) REVERT: B 267 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.6200 (p0) REVERT: C 23 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.4992 (mt0) REVERT: D 127 MET cc_start: 0.5596 (tpp) cc_final: 0.5076 (mmp) REVERT: E 1 MET cc_start: 0.1502 (mmm) cc_final: -0.0180 (mmt) REVERT: E 101 HIS cc_start: 0.5521 (OUTLIER) cc_final: 0.4967 (m170) REVERT: E 167 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7918 (tp) REVERT: E 181 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6639 (mtt90) REVERT: F 212 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5539 (mt-10) REVERT: F 274 THR cc_start: 0.5657 (OUTLIER) cc_final: 0.5455 (m) REVERT: G 48 MET cc_start: 0.6152 (mmt) cc_final: 0.5472 (mmt) REVERT: G 68 LYS cc_start: 0.6893 (pttt) cc_final: 0.6069 (mmmt) REVERT: G 135 ARG cc_start: 0.5721 (mtt-85) cc_final: 0.5514 (mtm180) REVERT: G 311 ILE cc_start: 0.7042 (mm) cc_final: 0.6726 (mm) outliers start: 43 outliers final: 30 residues processed: 209 average time/residue: 0.3022 time to fit residues: 96.7929 Evaluate side-chains 197 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 55 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 = 0.4674 r_free = 0.4674 target = 0.176159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.137670 restraints weight = 76831.518| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.84 r_work: 0.4055 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 1.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19041 Z= 0.171 Angle : 0.794 13.058 26142 Z= 0.370 Chirality : 0.054 0.553 3032 Planarity : 0.006 0.052 3181 Dihedral : 16.155 177.522 3199 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.18), residues: 2198 helix: -0.27 (0.20), residues: 657 sheet: -0.48 (0.24), residues: 476 loop : -2.07 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 272 TYR 0.016 0.002 TYR G 314 PHE 0.020 0.002 PHE F 232 TRP 0.012 0.002 TRP B 66 HIS 0.008 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19041) covalent geometry : angle 0.79393 / 0.37 (26142) hydrogen bonds : bond 0.04137 / 2.77 ( 726) hydrogen bonds : angle 5.47638 / 3.79 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: A 272 ARG cc_start: 0.5496 (mtm-85) cc_final: 0.5224 (mtt180) REVERT: B 259 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5963 (ppt170) REVERT: C 23 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.4990 (mt0) REVERT: D 83 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7506 (p) REVERT: E 1 MET cc_start: 0.1425 (mmm) cc_final: -0.0248 (mmt) REVERT: E 26 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7723 (ptt-90) REVERT: E 167 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8009 (tp) REVERT: E 181 ARG cc_start: 0.6897 (mtm-85) cc_final: 0.6694 (mtt90) REVERT: F 59 ASN cc_start: 0.6675 (m-40) cc_final: 0.6393 (m110) REVERT: F 212 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.5751 (mt-10) REVERT: F 274 THR cc_start: 0.5768 (OUTLIER) cc_final: 0.5510 (m) REVERT: G 48 MET cc_start: 0.6209 (mmt) cc_final: 0.5535 (mmt) REVERT: G 68 LYS cc_start: 0.6877 (pttt) cc_final: 0.6085 (mmmt) REVERT: G 135 ARG cc_start: 0.5918 (mtt-85) cc_final: 0.5715 (mtm180) REVERT: G 311 ILE cc_start: 0.6911 (mm) cc_final: 0.6449 (mm) outliers start: 51 outliers final: 38 residues processed: 209 average time/residue: 0.3010 time to fit residues: 94.5410 Evaluate side-chains 204 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 228 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 55 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 = 0.4761 r_free = 0.4761 target = 0.183364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.150153 restraints weight = 79404.045| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.35 r_work: 0.4120 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 1.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19041 Z= 0.126 Angle : 0.729 11.821 26142 Z= 0.335 Chirality : 0.051 0.526 3032 Planarity : 0.006 0.097 3181 Dihedral : 16.046 175.961 3199 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.42 % Allowed : 20.05 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2198 helix: -0.04 (0.21), residues: 662 sheet: -0.35 (0.25), residues: 468 loop : -1.93 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 272 TYR 0.017 0.001 TYR F 314 PHE 0.021 0.001 PHE F 232 TRP 0.010 0.001 TRP B 66 HIS 0.006 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19041) covalent geometry : angle 0.72908 / 0.34 (26142) hydrogen bonds : bond 0.03734 / 2.49 ( 726) hydrogen bonds : angle 5.29675 / 3.66 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9376.84 seconds wall clock time: 159 minutes 11.09 seconds (9551.09 seconds total)