Starting phenix.real_space_refine on Mon Jul 6 15:59:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ane_15540/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_2026/8ane_15540.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ane_15540/07_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-dev-6108/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: {'RNA': 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: 5.35, per 1000 atoms: 0.15 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: 2.51 Conformation dependent library (CDL) restraints added in 847.6 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: 7.40 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: 8.07 Time building geometry restraints manager: 3.46 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: 61763 2.15 - 4.30: 5295 4.30 - 6.45: 549 6.45 - 8.60: 83 8.60 - 10.74: 6 Bond angle restraints: 67696 Sorted by residual: angle pdb=" O4' U R 58 " pdb=" C1' U R 58 " pdb=" C2' U R 58 " ideal model delta sigma weight residual 107.60 102.44 5.16 1.00e+00 1.00e+00 2.66e+01 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=" C2' U R 58 " pdb=" C1' U R 58 " pdb=" N1 U R 58 " ideal model delta sigma weight residual 112.00 119.68 -7.68 1.50e+00 4.44e-01 2.62e+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=" 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: 16562 35.71 - 71.42: 564 71.42 - 107.14: 27 107.14 - 142.85: 5 142.85 - 178.56: 7 Dihedral angle restraints: 17165 sinusoidal: 10025 harmonic: 7140 Sorted by residual: dihedral pdb=" O4' C R 51 " pdb=" C1' C R 51 " pdb=" N1 C R 51 " pdb=" C2 C R 51 " ideal model delta sinusoidal sigma weight residual 200.00 54.20 145.80 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" O4' U R 33 " pdb=" C1' U R 33 " pdb=" N1 U R 33 " pdb=" C2 U R 33 " ideal model delta sinusoidal sigma weight residual 200.00 59.86 140.14 1 1.50e+01 4.44e-03 7.54e+01 dihedral pdb=" O4' C R 32 " pdb=" C1' C R 32 " pdb=" N1 C R 32 " pdb=" C2 C R 32 " ideal model delta sinusoidal sigma weight residual 200.00 70.42 129.58 1 1.50e+01 4.44e-03 6.99e+01 ... (remaining 17162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2230 0.039 - 0.078: 580 0.078 - 0.118: 163 0.118 - 0.157: 57 0.157 - 0.196: 2 Chirality restraints: 3032 Sorted by residual: chirality pdb=" C3' G R 42 " pdb=" C4' G R 42 " pdb=" O3' G R 42 " pdb=" C2' G R 42 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" C1' C R 29 " pdb=" O4' C R 29 " pdb=" C2' C R 29 " pdb=" N1 C R 29 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.82e-01 ... (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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 37.590 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- 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= 0.142 Angle : 0.645 7.681 26142 Z= 0.342 Chirality : 0.042 0.196 3032 Planarity : 0.006 0.066 3181 Dihedral : 15.689 178.561 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 0.00279 / 0.14 (19041) covalent geometry : angle 0.64465 / 0.34 (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 : 0.813 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: 0.3641 time to fit residues: 220.4485 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 : 0.897 ------------------------------------------------------------------------------- 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... B 59 ASN C 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 = 0.5265 r_free = 0.5265 target = 0.239748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.211823 restraints weight = 85694.791| |-----------------------------------------------------------------------------| r_work (start): 0.4988 rms_B_bonded: 2.13 r_work: 0.4837 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4730 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19041 Z= 0.188 Angle : 0.740 8.463 26142 Z= 0.376 Chirality : 0.044 0.237 3032 Planarity : 0.006 0.093 3181 Dihedral : 14.739 172.787 3214 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.20 % Allowed : 13.46 % Favored : 84.34 % 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: -1.47 (0.17), residues: 2198 helix: -0.36 (0.19), residues: 687 sheet: 0.26 (0.24), residues: 425 loop : -1.92 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 164 TYR 0.015 0.002 TYR D 221 PHE 0.015 0.002 PHE G 208 TRP 0.010 0.002 TRP F 279 HIS 0.009 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (19041) covalent geometry : angle 0.73956 / 0.38 (26142) hydrogen bonds : bond 0.04621 / 3.05 ( 726) hydrogen bonds : angle 6.00289 / 4.17 ( 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 320 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.967 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: A 269 GLN cc_start: 0.2917 (mp10) cc_final: 0.2585 (mp10) REVERT: B 48 MET cc_start: 0.4710 (mmt) cc_final: 0.4048 (ptt) REVERT: B 258 LEU cc_start: 0.6393 (mt) cc_final: 0.6188 (mt) REVERT: C 23 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.5820 (mm110) REVERT: E 1 MET cc_start: 0.1887 (mmm) cc_final: 0.0293 (mpp) REVERT: E 116 LEU cc_start: 0.7449 (tp) cc_final: 0.7221 (tt) REVERT: F 109 LEU cc_start: 0.5739 (tp) cc_final: 0.5427 (tp) REVERT: F 314 TYR cc_start: 0.3804 (t80) cc_final: 0.3005 (t80) REVERT: G 15 MET cc_start: 0.4899 (mpp) cc_final: 0.4685 (mpp) REVERT: G 159 GLU cc_start: 0.6078 (mp0) cc_final: 0.5719 (mt-10) REVERT: G 269 GLN cc_start: 0.4013 (mt0) cc_final: 0.3347 (tm-30) outliers start: 40 outliers final: 23 residues processed: 308 average time/residue: 0.3180 time to fit residues: 146.0729 Evaluate side-chains 235 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER 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 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 48 MET 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: 2.9990 chunk 111 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS B 269 GLN C 95 ASN C 147 ASN C 256 HIS F 55 GLN F 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.208629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.176348 restraints weight = 80935.741| |-----------------------------------------------------------------------------| r_work (start): 0.4662 rms_B_bonded: 2.68 r_work: 0.4475 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4363 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 19041 Z= 0.246 Angle : 0.854 15.159 26142 Z= 0.442 Chirality : 0.050 0.369 3032 Planarity : 0.009 0.210 3181 Dihedral : 14.932 179.300 3207 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 3.57 % Allowed : 15.05 % Favored : 81.37 % 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: -1.99 (0.17), residues: 2198 helix: -0.53 (0.20), residues: 646 sheet: -0.75 (0.23), residues: 479 loop : -2.10 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG A 303 TYR 0.020 0.003 TYR E 248 PHE 0.018 0.003 PHE A 304 TRP 0.027 0.003 TRP G 73 HIS 0.009 0.002 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (19041) covalent geometry : angle 0.85370 / 0.44 (26142) hydrogen bonds : bond 0.05851 / 3.79 ( 726) hydrogen bonds : angle 6.28986 / 4.38 ( 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 310 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.995 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: A 114 LYS cc_start: 0.2028 (mtmt) cc_final: 0.1724 (ptpp) REVERT: A 205 ASN cc_start: 0.6691 (m-40) cc_final: 0.6436 (m-40) REVERT: B 18 ASP cc_start: 0.5532 (p0) cc_final: 0.5242 (p0) REVERT: B 48 MET cc_start: 0.4534 (mmt) cc_final: 0.4110 (ptt) REVERT: B 60 ARG cc_start: 0.6403 (mtt-85) cc_final: 0.6130 (mtt-85) REVERT: B 311 ILE cc_start: 0.7005 (mp) cc_final: 0.6208 (mt) REVERT: C 311 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8011 (mt) REVERT: E 1 MET cc_start: 0.2231 (mmm) cc_final: 0.0160 (mpp) REVERT: E 117 PHE cc_start: 0.7569 (t80) cc_final: 0.7326 (t80) REVERT: E 141 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5226 (mp) REVERT: E 190 ASN cc_start: 0.2786 (t0) cc_final: 0.2357 (p0) REVERT: F 16 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: F 169 ARG cc_start: 0.6317 (mtt90) cc_final: 0.6056 (mtp180) REVERT: F 181 ARG cc_start: 0.5413 (mpp80) cc_final: 0.4916 (mtt-85) REVERT: G 68 LYS cc_start: 0.6873 (pttt) cc_final: 0.6073 (mmmt) REVERT: G 135 ARG cc_start: 0.5308 (mtt-85) cc_final: 0.4837 (mtm180) outliers start: 65 outliers final: 36 residues processed: 297 average time/residue: 0.3703 time to fit residues: 160.9081 Evaluate side-chains 223 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 154 PHE 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 25 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 188 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 96 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 18 ASP 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 E residue 35 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 141 LEU Chi-restraints excluded: chain E residue 188 VAL 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 185 SER Chi-restraints excluded: chain F residue 188 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 204 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN B 23 GLN B 59 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.199861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.164437 restraints weight = 79883.589| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.53 r_work: 0.4415 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4302 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.8060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 19041 Z= 0.199 Angle : 0.744 6.996 26142 Z= 0.383 Chirality : 0.046 0.352 3032 Planarity : 0.007 0.153 3181 Dihedral : 14.692 173.263 3207 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.80 % Allowed : 17.58 % Favored : 79.62 % 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: -1.88 (0.17), residues: 2198 helix: -0.45 (0.20), residues: 664 sheet: -0.43 (0.24), residues: 457 loop : -2.16 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG C 164 TYR 0.012 0.002 TYR F 248 PHE 0.014 0.002 PHE A 208 TRP 0.014 0.002 TRP C 73 HIS 0.012 0.002 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (19041) covalent geometry : angle 0.74423 / 0.38 (26142) hydrogen bonds : bond 0.04542 / 2.96 ( 726) hydrogen bonds : angle 5.81758 / 4.04 ( 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 256 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.957 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: A 1 MET cc_start: 0.0205 (tpt) cc_final: -0.2255 (mmp) REVERT: A 131 PRO cc_start: 0.5825 (Cg_endo) cc_final: 0.5583 (Cg_exo) REVERT: A 132 VAL cc_start: 0.5637 (m) cc_final: 0.5322 (t) REVERT: A 205 ASN cc_start: 0.6735 (m-40) cc_final: 0.6474 (m-40) REVERT: A 269 GLN cc_start: 0.3721 (mp10) cc_final: 0.3297 (mp-120) REVERT: B 48 MET cc_start: 0.4835 (mmm) cc_final: 0.4391 (ptt) REVERT: B 69 ASP cc_start: 0.5937 (t70) cc_final: 0.5642 (m-30) REVERT: C 23 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.5425 (mt0) REVERT: C 298 VAL cc_start: 0.5491 (t) cc_final: 0.5227 (p) REVERT: E 1 MET cc_start: 0.2230 (mmm) cc_final: 0.0139 (mpp) REVERT: E 117 PHE cc_start: 0.7479 (t80) cc_final: 0.7179 (t80) REVERT: E 141 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5248 (mp) REVERT: F 109 LEU cc_start: 0.6248 (tp) cc_final: 0.6033 (tp) REVERT: F 169 ARG cc_start: 0.6329 (mtt90) cc_final: 0.5785 (mtp180) REVERT: F 181 ARG cc_start: 0.5464 (mpp80) cc_final: 0.4848 (mtt-85) REVERT: F 185 SER cc_start: 0.7092 (m) cc_final: 0.6486 (p) REVERT: F 212 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5908 (mt-10) REVERT: F 261 ARG cc_start: 0.6299 (ttm110) cc_final: 0.5819 (mtm-85) REVERT: G 68 LYS cc_start: 0.6809 (pttt) cc_final: 0.5982 (mmmt) REVERT: G 135 ARG cc_start: 0.5457 (mtt-85) cc_final: 0.5095 (mtm180) outliers start: 51 outliers final: 32 residues processed: 249 average time/residue: 0.3412 time to fit residues: 127.8542 Evaluate side-chains 211 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 188 VAL 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 144 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 64 VAL 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 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 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 295 ILE 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 228 GLN 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 Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 137 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.194824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.161207 restraints weight = 79162.498| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 2.55 r_work: 0.4262 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19041 Z= 0.169 Angle : 0.673 6.891 26142 Z= 0.348 Chirality : 0.043 0.196 3032 Planarity : 0.006 0.060 3181 Dihedral : 14.721 176.735 3207 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.91 % Allowed : 18.90 % Favored : 78.19 % 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: -1.79 (0.18), residues: 2198 helix: -0.29 (0.21), residues: 663 sheet: -0.72 (0.24), residues: 483 loop : -2.00 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 164 TYR 0.018 0.002 TYR B 314 PHE 0.046 0.002 PHE F 232 TRP 0.016 0.002 TRP G 73 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (19041) covalent geometry : angle 0.67287 / 0.35 (26142) hydrogen bonds : bond 0.04413 / 2.92 ( 726) hydrogen bonds : angle 5.68072 / 3.93 ( 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 243 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.927 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: B 48 MET cc_start: 0.4807 (mmm) cc_final: 0.4334 (ptt) REVERT: C 145 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6336 (p0) REVERT: D 83 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7310 (p) REVERT: E 1 MET cc_start: 0.1594 (mmm) cc_final: -0.0459 (mpp) REVERT: E 117 PHE cc_start: 0.7268 (t80) cc_final: 0.7002 (t80) REVERT: E 141 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.4956 (mp) REVERT: E 179 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6116 (m-30) REVERT: F 181 ARG cc_start: 0.5552 (mpp80) cc_final: 0.4736 (mtt-85) REVERT: F 185 SER cc_start: 0.7222 (m) cc_final: 0.6610 (p) REVERT: F 261 ARG cc_start: 0.6221 (ttm110) cc_final: 0.5843 (mtm-85) REVERT: G 15 MET cc_start: 0.6297 (mpp) cc_final: 0.5852 (mpp) REVERT: G 68 LYS cc_start: 0.6877 (pttt) cc_final: 0.5977 (mmmt) REVERT: G 85 VAL cc_start: 0.6795 (t) cc_final: 0.6355 (m) REVERT: G 135 ARG cc_start: 0.5873 (mtt-85) cc_final: 0.5452 (mtm180) outliers start: 53 outliers final: 32 residues processed: 235 average time/residue: 0.3037 time to fit residues: 109.4229 Evaluate side-chains 200 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 PHE 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 30 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 83 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 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 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 57 MET 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 Chi-restraints excluded: chain G residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 220 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 101 HIS C 59 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 HIS D 190 ASN E 59 ASN F 228 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.181570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.146716 restraints weight = 80685.567| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.63 r_work: 0.4093 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 1.0368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19041 Z= 0.261 Angle : 0.866 11.040 26142 Z= 0.453 Chirality : 0.050 0.253 3032 Planarity : 0.009 0.118 3181 Dihedral : 15.124 172.673 3201 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.90 % Rotamer: Outliers : 4.29 % Allowed : 19.01 % Favored : 76.70 % 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: -2.47 (0.17), residues: 2198 helix: -0.93 (0.20), residues: 639 sheet: -0.93 (0.24), residues: 494 loop : -2.45 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 303 TYR 0.020 0.003 TYR B 40 PHE 0.048 0.003 PHE F 232 TRP 0.018 0.003 TRP B 66 HIS 0.014 0.003 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (19041) covalent geometry : angle 0.86615 / 0.45 (26142) hydrogen bonds : bond 0.05236 / 3.49 ( 726) hydrogen bonds : angle 6.13233 / 4.26 ( 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 274 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 0.597 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 176 GLU cc_start: 0.5431 (pp20) cc_final: 0.5064 (mt-10) REVERT: B 143 LYS cc_start: 0.3806 (OUTLIER) cc_final: 0.3186 (mmtt) REVERT: B 259 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5846 (ppt170) REVERT: B 310 THR cc_start: 0.6475 (OUTLIER) cc_final: 0.6220 (p) REVERT: C 23 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.5018 (mt0) REVERT: C 230 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5888 (mtm-85) REVERT: D 83 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7599 (p) REVERT: E 1 MET cc_start: 0.1112 (mmm) cc_final: -0.0469 (mmt) REVERT: E 141 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5351 (mp) REVERT: E 179 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6405 (m-30) REVERT: E 190 ASN cc_start: 0.3197 (OUTLIER) cc_final: 0.2471 (p0) REVERT: F 117 PHE cc_start: 0.7368 (t80) cc_final: 0.7054 (t80) REVERT: F 212 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: G 68 LYS cc_start: 0.6842 (pttt) cc_final: 0.5979 (mmmt) REVERT: G 85 VAL cc_start: 0.7090 (t) cc_final: 0.6659 (m) outliers start: 78 outliers final: 46 residues processed: 266 average time/residue: 0.3013 time to fit residues: 121.8832 Evaluate side-chains 222 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 165 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 30 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 THR 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 103 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 64 VAL 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 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 212 GLU 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 16 GLU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 284 LEU 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: 0.0770 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.184831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.150013 restraints weight = 79586.841| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.31 r_work: 0.4134 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 1.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19041 Z= 0.131 Angle : 0.639 6.466 26142 Z= 0.330 Chirality : 0.042 0.203 3032 Planarity : 0.006 0.059 3181 Dihedral : 14.823 174.916 3197 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.42 % Allowed : 20.49 % Favored : 77.09 % 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: -1.87 (0.18), residues: 2198 helix: -0.32 (0.21), residues: 657 sheet: -0.67 (0.24), residues: 481 loop : -2.13 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 303 TYR 0.018 0.001 TYR B 40 PHE 0.027 0.002 PHE F 232 TRP 0.014 0.001 TRP B 66 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19041) covalent geometry : angle 0.63877 / 0.33 (26142) hydrogen bonds : bond 0.04146 / 2.75 ( 726) hydrogen bonds : angle 5.55096 / 3.84 ( 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 217 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.764 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 265 ASP cc_start: 0.5862 (m-30) cc_final: 0.5343 (m-30) REVERT: B 275 ARG cc_start: 0.3454 (OUTLIER) cc_final: 0.2784 (mmt90) REVERT: E 1 MET cc_start: 0.1579 (mmm) cc_final: -0.0245 (mmt) REVERT: E 117 PHE cc_start: 0.7242 (t80) cc_final: 0.7012 (t80) REVERT: E 141 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5168 (mp) REVERT: E 167 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7856 (tt) REVERT: E 179 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: F 117 PHE cc_start: 0.7227 (t80) cc_final: 0.7004 (t80) REVERT: F 135 ARG cc_start: 0.5549 (mpp80) cc_final: 0.5315 (mtm110) REVERT: F 274 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5427 (m) REVERT: G 48 MET cc_start: 0.5213 (mmt) cc_final: 0.4938 (mmt) REVERT: G 68 LYS cc_start: 0.6796 (pttt) cc_final: 0.5947 (mmmt) REVERT: G 135 ARG cc_start: 0.5962 (mtt-85) cc_final: 0.5743 (mtm180) outliers start: 44 outliers final: 29 residues processed: 213 average time/residue: 0.3178 time to fit residues: 102.7922 Evaluate side-chains 197 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 180 VAL 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 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 188 VAL 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 95 ASN Chi-restraints excluded: chain G residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 42 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 195 optimal weight: 0.0060 chunk 170 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN C 126 HIS ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.181924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.146435 restraints weight = 79773.822| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.64 r_work: 0.4096 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 1.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19041 Z= 0.160 Angle : 0.654 6.502 26142 Z= 0.338 Chirality : 0.042 0.198 3032 Planarity : 0.006 0.052 3181 Dihedral : 14.730 173.021 3197 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.75 % Allowed : 20.88 % Favored : 76.37 % 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: -1.83 (0.18), residues: 2198 helix: -0.28 (0.21), residues: 657 sheet: -0.67 (0.24), residues: 493 loop : -2.11 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 166 TYR 0.014 0.001 TYR F 107 PHE 0.026 0.002 PHE F 232 TRP 0.012 0.001 TRP B 66 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (19041) covalent geometry : angle 0.65414 / 0.34 (26142) hydrogen bonds : bond 0.04116 / 2.74 ( 726) hydrogen bonds : angle 5.49902 / 3.81 ( 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 213 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.988 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: A 265 ASP cc_start: 0.6135 (m-30) cc_final: 0.5597 (m-30) REVERT: A 272 ARG cc_start: 0.5777 (mtm-85) cc_final: 0.5507 (mtt180) REVERT: B 259 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.5854 (ppt170) REVERT: B 275 ARG cc_start: 0.3505 (OUTLIER) cc_final: 0.3146 (mmt90) REVERT: D 83 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7440 (p) REVERT: E 1 MET cc_start: 0.1333 (mmm) cc_final: -0.0351 (mmt) REVERT: E 117 PHE cc_start: 0.7136 (t80) cc_final: 0.6908 (t80) REVERT: E 141 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5289 (mp) REVERT: E 167 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7981 (tp) REVERT: E 179 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: F 117 PHE cc_start: 0.7326 (t80) cc_final: 0.7059 (t80) REVERT: F 261 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6175 (mtm-85) REVERT: F 274 THR cc_start: 0.5677 (OUTLIER) cc_final: 0.5459 (m) REVERT: G 48 MET cc_start: 0.5218 (mmt) cc_final: 0.4905 (mmt) REVERT: G 68 LYS cc_start: 0.6845 (pttt) cc_final: 0.5994 (mmmt) REVERT: G 311 ILE cc_start: 0.6817 (mm) cc_final: 0.6348 (mm) outliers start: 50 outliers final: 34 residues processed: 207 average time/residue: 0.3242 time to fit residues: 99.6285 Evaluate side-chains 201 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 180 VAL 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 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 261 ARG 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 Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU 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: 3.9990 chunk 160 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 123 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.183993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.149053 restraints weight = 79622.785| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.52 r_work: 0.4129 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 1.1072 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= 0.118 Angle : 0.597 6.740 26142 Z= 0.305 Chirality : 0.041 0.208 3032 Planarity : 0.005 0.055 3181 Dihedral : 14.619 173.250 3197 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.36 % Allowed : 21.32 % Favored : 76.32 % 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: -1.51 (0.18), residues: 2198 helix: 0.01 (0.21), residues: 657 sheet: -0.31 (0.25), residues: 465 loop : -2.00 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 303 TYR 0.013 0.001 TYR B 40 PHE 0.018 0.001 PHE F 232 TRP 0.010 0.001 TRP B 66 HIS 0.004 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (19041) covalent geometry : angle 0.59689 / 0.31 (26142) hydrogen bonds : bond 0.03740 / 2.48 ( 726) hydrogen bonds : angle 5.25744 / 3.62 ( 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 : 1.107 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 265 ASP cc_start: 0.6270 (m-30) cc_final: 0.5869 (m-30) REVERT: A 272 ARG cc_start: 0.5785 (mtm-85) cc_final: 0.5439 (mtt180) REVERT: B 77 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 191 ASP cc_start: 0.4788 (t0) cc_final: 0.4560 (t0) REVERT: B 259 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.5801 (ppt170) REVERT: B 275 ARG cc_start: 0.3623 (OUTLIER) cc_final: 0.3248 (mmt90) REVERT: D 154 PHE cc_start: 0.7913 (t80) cc_final: 0.7649 (t80) REVERT: E 1 MET cc_start: 0.1298 (mmm) cc_final: -0.0355 (mmt) REVERT: E 141 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5212 (mp) REVERT: E 167 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7825 (tt) REVERT: F 57 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7490 (mmm) REVERT: F 117 PHE cc_start: 0.7204 (t80) cc_final: 0.6939 (t80) REVERT: F 261 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6202 (mtm-85) REVERT: G 48 MET cc_start: 0.5255 (mmt) cc_final: 0.5003 (mmt) REVERT: G 68 LYS cc_start: 0.6915 (pttt) cc_final: 0.6068 (mmmt) outliers start: 43 outliers final: 27 residues processed: 208 average time/residue: 0.3140 time to fit residues: 98.6028 Evaluate side-chains 196 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 180 VAL 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 126 HIS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 261 ARG 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 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 198 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 210 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.185088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.151442 restraints weight = 79331.498| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.35 r_work: 0.4144 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 1.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19041 Z= 0.105 Angle : 0.579 7.022 26142 Z= 0.293 Chirality : 0.040 0.204 3032 Planarity : 0.005 0.052 3181 Dihedral : 14.494 172.016 3197 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.70 % Allowed : 22.14 % Favored : 76.15 % 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: -1.33 (0.18), residues: 2198 helix: 0.13 (0.21), residues: 665 sheet: -0.18 (0.25), residues: 465 loop : -1.89 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 78 TYR 0.018 0.001 TYR F 314 PHE 0.019 0.001 PHE F 232 TRP 0.010 0.001 TRP B 66 HIS 0.003 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (19041) covalent geometry : angle 0.57943 / 0.29 (26142) hydrogen bonds : bond 0.03484 / 2.31 ( 726) hydrogen bonds : angle 5.10147 / 3.51 ( 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 197 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.759 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 265 ASP cc_start: 0.6225 (m-30) cc_final: 0.5836 (m-30) REVERT: A 272 ARG cc_start: 0.5852 (mtm-85) cc_final: 0.5517 (mtt180) REVERT: B 77 LEU cc_start: 0.7116 (tp) cc_final: 0.6666 (mp) REVERT: B 191 ASP cc_start: 0.4532 (t0) cc_final: 0.4031 (t0) REVERT: B 259 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.5747 (ppt170) REVERT: B 275 ARG cc_start: 0.3565 (OUTLIER) cc_final: 0.3164 (mmt90) REVERT: C 180 VAL cc_start: 0.7349 (m) cc_final: 0.7098 (m) REVERT: C 230 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5941 (mtm-85) REVERT: D 154 PHE cc_start: 0.7881 (t80) cc_final: 0.7620 (t80) REVERT: E 1 MET cc_start: 0.1382 (mmm) cc_final: -0.0313 (mmt) REVERT: E 167 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7801 (tt) REVERT: F 117 PHE cc_start: 0.7216 (t80) cc_final: 0.6962 (t80) REVERT: F 261 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6177 (mtm-85) REVERT: G 48 MET cc_start: 0.5159 (mmt) cc_final: 0.4878 (mmt) REVERT: G 68 LYS cc_start: 0.6903 (pttt) cc_final: 0.6062 (mmmt) REVERT: G 166 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7722 (ptp90) outliers start: 31 outliers final: 18 residues processed: 192 average time/residue: 0.3129 time to fit residues: 91.7118 Evaluate side-chains 178 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain D residue 180 VAL 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 126 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.148793 restraints weight = 79509.113| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.36 r_work: 0.4112 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 1.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19041 Z= 0.127 Angle : 0.613 11.685 26142 Z= 0.310 Chirality : 0.041 0.207 3032 Planarity : 0.005 0.079 3181 Dihedral : 14.509 172.062 3197 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.92 % Allowed : 22.14 % Favored : 75.93 % 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: -1.36 (0.18), residues: 2198 helix: 0.13 (0.21), residues: 663 sheet: -0.32 (0.24), residues: 480 loop : -1.87 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 135 TYR 0.016 0.001 TYR F 314 PHE 0.020 0.001 PHE F 232 TRP 0.011 0.001 TRP B 66 HIS 0.015 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19041) covalent geometry : angle 0.61290 / 0.31 (26142) hydrogen bonds : bond 0.03679 / 2.44 ( 726) hydrogen bonds : angle 5.15402 / 3.56 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10454.82 seconds wall clock time: 177 minutes 28.71 seconds (10648.71 seconds total)