Starting phenix.real_space_refine on Tue Aug 26 12:31:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.map" model { file = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ane_15540/08_2025/8ane_15540.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 66 5.49 5 S 56 5.16 5 C 11536 2.51 5 N 3263 2.21 5 O 3624 1.98 5 H 18195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.63, 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: 3.00 Conformation dependent library (CDL) restraints added in 904.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 36 sheets defined 36.5% alpha, 20.1% beta 2 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 5.84 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: 7.90 Time building geometry restraints manager: 4.03 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: 16715 35.71 - 71.42: 679 71.42 - 107.14: 46 107.14 - 142.85: 5 142.85 - 178.56: 7 Dihedral angle restraints: 17452 sinusoidal: 10312 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 17449 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: 2.680 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: 0.220 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.150 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 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 : 17.194 178.561 7647 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 aren 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 covalent geometry : bond 0.00279 (19041) covalent geometry : angle 0.64465 (26142) hydrogen bonds : bond 0.16549 ( 726) hydrogen bonds : angle 7.78717 ( 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 : 0.907 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: 0.3691 time to fit residues: 220.9205 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 : 0.879 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.240247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.212437 restraints weight = 85855.337| |-----------------------------------------------------------------------------| r_work (start): 0.4994 rms_B_bonded: 2.17 r_work: 0.4833 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4733 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19041 Z= 0.185 Angle : 0.727 8.297 26142 Z= 0.370 Chirality : 0.043 0.239 3032 Planarity : 0.006 0.095 3181 Dihedral : 18.174 173.736 3464 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.31 % Allowed : 13.19 % Favored : 84.51 % 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 aren not related in a simple way. whole: -1.46 (0.17), residues: 2198 helix: -0.36 (0.19), residues: 687 sheet: 0.28 (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 0.014 0.002 TYR D 221 PHE 0.015 0.002 PHE G 208 TRP 0.010 0.002 TRP F 279 HIS 0.008 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00409 (19041) covalent geometry : angle 0.72701 (26142) hydrogen bonds : bond 0.04637 ( 726) hydrogen bonds : angle 6.03303 ( 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 323 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.000 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: A 269 GLN cc_start: 0.2907 (mp10) cc_final: 0.2560 (mp10) REVERT: B 48 MET cc_start: 0.4705 (mmt) cc_final: 0.4034 (ptt) REVERT: C 23 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5807 (mm110) REVERT: E 1 MET cc_start: 0.1883 (mmm) cc_final: 0.0299 (mpp) REVERT: E 116 LEU cc_start: 0.7455 (tp) cc_final: 0.7216 (tt) REVERT: F 109 LEU cc_start: 0.5713 (tp) cc_final: 0.5429 (tp) REVERT: F 314 TYR cc_start: 0.3769 (t80) cc_final: 0.2982 (t80) REVERT: G 159 GLU cc_start: 0.6066 (mp0) cc_final: 0.5711 (mt-10) REVERT: G 269 GLN cc_start: 0.4004 (mt0) cc_final: 0.3351 (tm-30) outliers start: 42 outliers final: 25 residues processed: 310 average time/residue: 0.3915 time to fit residues: 177.3334 Evaluate side-chains 236 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 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: 3.9990 chunk 111 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 188 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 147 ASN C 256 HIS F 228 GLN F 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.222767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.189737 restraints weight = 82357.769| |-----------------------------------------------------------------------------| r_work (start): 0.4785 rms_B_bonded: 2.68 r_work: 0.4652 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4541 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 19041 Z= 0.187 Angle : 0.696 7.667 26142 Z= 0.358 Chirality : 0.044 0.241 3032 Planarity : 0.007 0.185 3181 Dihedral : 18.034 178.331 3459 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.36 % Allowed : 15.16 % Favored : 82.47 % 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 aren not related in a simple way. whole: -1.36 (0.17), residues: 2198 helix: -0.02 (0.20), residues: 671 sheet: -0.03 (0.24), residues: 433 loop : -1.87 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 303 TYR 0.028 0.002 TYR A 213 PHE 0.034 0.002 PHE D 154 TRP 0.023 0.002 TRP G 73 HIS 0.006 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00412 (19041) covalent geometry : angle 0.69582 (26142) hydrogen bonds : bond 0.05022 ( 726) hydrogen bonds : angle 5.81129 ( 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 276 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.4257 (t) cc_final: 0.4046 (t) REVERT: A 205 ASN cc_start: 0.6444 (m-40) cc_final: 0.6207 (m-40) REVERT: A 272 ARG cc_start: 0.5898 (ttm110) cc_final: 0.5646 (mtm-85) REVERT: B 18 ASP cc_start: 0.5341 (p0) cc_final: 0.5004 (p0) REVERT: B 48 MET cc_start: 0.4549 (mmt) cc_final: 0.3926 (ptt) REVERT: C 180 VAL cc_start: 0.7339 (m) cc_final: 0.7043 (m) REVERT: E 1 MET cc_start: 0.2150 (mmm) cc_final: 0.0273 (mpp) REVERT: E 117 PHE cc_start: 0.7478 (t80) cc_final: 0.7255 (t80) REVERT: F 15 MET cc_start: 0.4931 (mmm) cc_final: 0.4663 (mmm) REVERT: F 272 ARG cc_start: 0.5395 (ptm160) cc_final: 0.5167 (ptm160) REVERT: G 135 ARG cc_start: 0.5096 (mtt-85) cc_final: 0.4763 (mtm180) REVERT: G 159 GLU cc_start: 0.6110 (mp0) cc_final: 0.5822 (mt-10) outliers start: 43 outliers final: 27 residues processed: 270 average time/residue: 0.3741 time to fit residues: 149.1431 Evaluate side-chains 217 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 49 LEU 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 193 VAL Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 185 SER 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: 2.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS C 269 GLN ** F 147 ASN ** 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 = 0.5013 r_free = 0.5013 target = 0.208692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.174177 restraints weight = 80349.766| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 2.33 r_work: 0.4498 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4385 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 19041 Z= 0.186 Angle : 0.717 8.079 26142 Z= 0.367 Chirality : 0.045 0.232 3032 Planarity : 0.006 0.065 3181 Dihedral : 17.912 172.402 3455 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.36 % Allowed : 16.70 % Favored : 80.93 % 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 aren not related in a simple way. whole: -1.50 (0.17), residues: 2198 helix: -0.03 (0.20), residues: 664 sheet: -0.35 (0.24), residues: 452 loop : -1.93 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 166 TYR 0.018 0.002 TYR B 40 PHE 0.028 0.002 PHE E 154 TRP 0.016 0.002 TRP C 73 HIS 0.009 0.002 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00428 (19041) covalent geometry : angle 0.71679 (26142) hydrogen bonds : bond 0.04322 ( 726) hydrogen bonds : angle 5.55407 ( 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 269 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 1.014 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: B 18 ASP cc_start: 0.5379 (p0) cc_final: 0.5052 (p0) REVERT: B 48 MET cc_start: 0.4649 (mmt) cc_final: 0.4217 (ptt) REVERT: B 69 ASP cc_start: 0.6189 (t70) cc_final: 0.5911 (m-30) REVERT: B 104 ASN cc_start: 0.5289 (OUTLIER) cc_final: 0.5035 (t0) REVERT: B 230 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5388 (mtm-85) REVERT: B 280 GLU cc_start: 0.5755 (mm-30) cc_final: 0.5398 (tp30) REVERT: B 309 VAL cc_start: 0.6491 (t) cc_final: 0.6034 (p) REVERT: C 311 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7973 (mt) REVERT: E 1 MET cc_start: 0.2168 (mmm) cc_final: 0.0156 (mpp) REVERT: E 117 PHE cc_start: 0.7535 (t80) cc_final: 0.7241 (t80) REVERT: F 109 LEU cc_start: 0.6244 (tp) cc_final: 0.6040 (tp) REVERT: F 181 ARG cc_start: 0.5273 (mpp80) cc_final: 0.4739 (mtt-85) REVERT: F 261 ARG cc_start: 0.5915 (ttm110) cc_final: 0.5632 (mtm-85) REVERT: G 15 MET cc_start: 0.5035 (mpp) cc_final: 0.4811 (mpp) REVERT: G 68 LYS cc_start: 0.6772 (pttt) cc_final: 0.5960 (mmmt) REVERT: G 85 VAL cc_start: 0.6479 (t) cc_final: 0.6061 (m) REVERT: G 135 ARG cc_start: 0.5296 (mtt-85) cc_final: 0.4533 (mtm180) REVERT: G 259 ARG cc_start: 0.6627 (mtp180) cc_final: 0.6031 (mtt90) outliers start: 43 outliers final: 28 residues processed: 260 average time/residue: 0.3914 time to fit residues: 148.6635 Evaluate side-chains 212 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 ILE 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 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 137 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 189 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.204634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.171522 restraints weight = 79621.510| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 2.31 r_work: 0.4441 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4329 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19041 Z= 0.143 Angle : 0.624 5.702 26142 Z= 0.321 Chirality : 0.042 0.183 3032 Planarity : 0.006 0.068 3181 Dihedral : 17.893 175.920 3455 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.25 % Allowed : 17.53 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2198 helix: 0.09 (0.21), residues: 666 sheet: -0.26 (0.25), residues: 449 loop : -1.81 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 164 TYR 0.016 0.001 TYR B 40 PHE 0.035 0.002 PHE D 154 TRP 0.014 0.001 TRP G 73 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00319 (19041) covalent geometry : angle 0.62413 (26142) hydrogen bonds : bond 0.04013 ( 726) hydrogen bonds : angle 5.46626 ( 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 244 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.059 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: B 60 ARG cc_start: 0.6441 (mtt-85) cc_final: 0.6076 (mtt-85) REVERT: B 69 ASP cc_start: 0.6171 (t70) cc_final: 0.5900 (m-30) REVERT: C 23 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.5506 (mt0) REVERT: C 180 VAL cc_start: 0.7547 (m) cc_final: 0.7313 (m) REVERT: C 298 VAL cc_start: 0.5494 (t) cc_final: 0.5141 (p) REVERT: E 1 MET cc_start: 0.2156 (mmm) cc_final: 0.0138 (mpp) REVERT: E 117 PHE cc_start: 0.7540 (t80) cc_final: 0.7230 (t80) REVERT: F 181 ARG cc_start: 0.5346 (mpp80) cc_final: 0.4800 (mtt-85) REVERT: F 185 SER cc_start: 0.6720 (OUTLIER) cc_final: 0.6248 (p) REVERT: F 261 ARG cc_start: 0.6005 (ttm110) cc_final: 0.5681 (mtm-85) REVERT: G 15 MET cc_start: 0.4923 (mpp) cc_final: 0.4628 (mpp) REVERT: G 68 LYS cc_start: 0.6819 (pttt) cc_final: 0.5951 (mmmt) REVERT: G 85 VAL cc_start: 0.6404 (t) cc_final: 0.5941 (m) REVERT: G 135 ARG cc_start: 0.5239 (mtt-85) cc_final: 0.4780 (mtm180) outliers start: 41 outliers final: 28 residues processed: 238 average time/residue: 0.3462 time to fit residues: 125.5785 Evaluate side-chains 214 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 220 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 190 ASN B 23 GLN B 59 ASN B 269 GLN C 59 ASN C 95 ASN C 147 ASN D 151 HIS D 190 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.189667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.156098 restraints weight = 79553.665| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.37 r_work: 0.4201 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.9359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19041 Z= 0.241 Angle : 0.811 8.939 26142 Z= 0.422 Chirality : 0.048 0.241 3032 Planarity : 0.008 0.113 3181 Dihedral : 18.227 172.838 3455 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.46 % Allowed : 17.47 % Favored : 79.07 % 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 aren not related in a simple way. whole: -2.01 (0.17), residues: 2198 helix: -0.61 (0.20), residues: 661 sheet: -0.70 (0.24), residues: 486 loop : -2.12 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 78 TYR 0.018 0.002 TYR E 248 PHE 0.024 0.003 PHE F 32 TRP 0.017 0.003 TRP C 73 HIS 0.014 0.002 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00552 (19041) covalent geometry : angle 0.81069 (26142) hydrogen bonds : bond 0.04859 ( 726) hydrogen bonds : angle 5.89721 ( 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 256 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1405 (tpt) cc_final: -0.0193 (tmm) REVERT: A 30 THR cc_start: 0.6064 (t) cc_final: 0.5807 (t) REVERT: A 48 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.4182 (ptm) REVERT: B 1 MET cc_start: 0.2470 (tpt) cc_final: 0.2075 (tpt) REVERT: B 60 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.6698 (mtt-85) REVERT: B 69 ASP cc_start: 0.6303 (t70) cc_final: 0.5484 (m-30) REVERT: B 269 GLN cc_start: 0.5663 (OUTLIER) cc_final: 0.5199 (mm110) REVERT: C 23 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.5009 (mt0) REVERT: D 83 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7426 (p) REVERT: E 1 MET cc_start: 0.1394 (mmm) cc_final: -0.0559 (mmt) REVERT: E 190 ASN cc_start: 0.3106 (OUTLIER) cc_final: 0.2462 (p0) REVERT: F 109 LEU cc_start: 0.6553 (tp) cc_final: 0.6310 (tp) REVERT: F 181 ARG cc_start: 0.5709 (mpp80) cc_final: 0.4849 (mtt-85) REVERT: F 212 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: F 261 ARG cc_start: 0.6449 (ttm110) cc_final: 0.5982 (mtm-85) REVERT: G 68 LYS cc_start: 0.6887 (pttt) cc_final: 0.6011 (mmmt) REVERT: G 85 VAL cc_start: 0.6679 (t) cc_final: 0.6134 (m) REVERT: G 135 ARG cc_start: 0.5697 (mtt-85) cc_final: 0.5312 (mtm180) outliers start: 63 outliers final: 38 residues processed: 245 average time/residue: 0.3416 time to fit residues: 126.1512 Evaluate side-chains 197 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 30 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 83 VAL 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 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 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 13 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 223 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 143 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.191066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.155068 restraints weight = 79722.328| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.71 r_work: 0.4202 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.9632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19041 Z= 0.129 Angle : 0.630 6.672 26142 Z= 0.323 Chirality : 0.042 0.194 3032 Planarity : 0.006 0.058 3181 Dihedral : 17.996 173.935 3451 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.47 % Allowed : 19.01 % Favored : 78.52 % 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 aren not related in a simple way. whole: -1.55 (0.18), residues: 2198 helix: -0.19 (0.20), residues: 663 sheet: -0.32 (0.25), residues: 453 loop : -1.89 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 252 TYR 0.008 0.001 TYR A 40 PHE 0.023 0.002 PHE F 232 TRP 0.013 0.001 TRP B 66 HIS 0.004 0.001 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00287 (19041) covalent geometry : angle 0.63002 (26142) hydrogen bonds : bond 0.03969 ( 726) hydrogen bonds : angle 5.47744 ( 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 214 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.921 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: A 1 MET cc_start: 0.1415 (tpt) cc_final: -0.0305 (tmm) REVERT: A 30 THR cc_start: 0.6237 (t) cc_final: 0.5968 (t) REVERT: B 1 MET cc_start: 0.2553 (tpt) cc_final: 0.2339 (tpt) REVERT: B 48 MET cc_start: 0.4846 (mmm) cc_final: 0.4386 (ptt) REVERT: B 143 LYS cc_start: 0.3916 (OUTLIER) cc_final: 0.2942 (mmtt) REVERT: B 274 THR cc_start: 0.6381 (m) cc_final: 0.6160 (p) REVERT: C 23 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.5077 (mt0) REVERT: E 1 MET cc_start: 0.1853 (mmm) cc_final: 0.1046 (ptm) REVERT: E 101 HIS cc_start: 0.5218 (OUTLIER) cc_final: 0.4763 (m170) REVERT: E 117 PHE cc_start: 0.7289 (t80) cc_final: 0.7011 (t80) REVERT: F 101 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.7159 (p-80) REVERT: F 181 ARG cc_start: 0.5732 (mpp80) cc_final: 0.4882 (mtt-85) REVERT: F 261 ARG cc_start: 0.6085 (ttm110) cc_final: 0.5808 (mtm-85) REVERT: G 68 LYS cc_start: 0.6855 (pttt) cc_final: 0.5947 (mmmt) REVERT: G 85 VAL cc_start: 0.6832 (t) cc_final: 0.6354 (m) REVERT: G 135 ARG cc_start: 0.5767 (mtt-85) cc_final: 0.5357 (mtm180) outliers start: 45 outliers final: 27 residues processed: 208 average time/residue: 0.3095 time to fit residues: 97.3533 Evaluate side-chains 191 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 304 PHE 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 23 GLN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 279 TRP Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 42 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 170 optimal weight: 0.0000 chunk 128 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.191132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.155296 restraints weight = 79309.366| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.85 r_work: 0.4200 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.9880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19041 Z= 0.120 Angle : 0.594 7.759 26142 Z= 0.301 Chirality : 0.040 0.183 3032 Planarity : 0.005 0.078 3181 Dihedral : 17.782 171.570 3451 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.70 % Allowed : 19.62 % Favored : 78.68 % 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 aren not related in a simple way. whole: -1.23 (0.18), residues: 2198 helix: 0.20 (0.21), residues: 660 sheet: -0.27 (0.25), residues: 468 loop : -1.74 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 164 TYR 0.025 0.001 TYR B 314 PHE 0.026 0.002 PHE F 232 TRP 0.011 0.001 TRP B 66 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00272 (19041) covalent geometry : angle 0.59360 (26142) hydrogen bonds : bond 0.03647 ( 726) hydrogen bonds : angle 5.19253 ( 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 203 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.5758 (mtm-85) cc_final: 0.5522 (mtt180) REVERT: B 18 ASP cc_start: 0.6000 (p0) cc_final: 0.5493 (p0) REVERT: B 48 MET cc_start: 0.4694 (mmm) cc_final: 0.4298 (ptt) REVERT: B 143 LYS cc_start: 0.3717 (OUTLIER) cc_final: 0.2886 (mmtt) REVERT: C 180 VAL cc_start: 0.7418 (m) cc_final: 0.7190 (m) REVERT: E 1 MET cc_start: 0.1913 (mmm) cc_final: -0.0212 (mmt) REVERT: E 101 HIS cc_start: 0.5079 (OUTLIER) cc_final: 0.4677 (m170) REVERT: E 117 PHE cc_start: 0.7266 (t80) cc_final: 0.6959 (t80) REVERT: F 261 ARG cc_start: 0.5991 (ttm110) cc_final: 0.5622 (mtm-85) REVERT: G 48 MET cc_start: 0.5921 (mmt) cc_final: 0.5712 (mmt) REVERT: G 68 LYS cc_start: 0.6807 (pttt) cc_final: 0.5970 (mmmt) REVERT: G 135 ARG cc_start: 0.5780 (mtt-85) cc_final: 0.5359 (mtm180) outliers start: 31 outliers final: 23 residues processed: 198 average time/residue: 0.3345 time to fit residues: 101.1004 Evaluate side-chains 185 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 192 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.191013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.153975 restraints weight = 79883.218| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.92 r_work: 0.4202 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 1.0084 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= 0.111 Angle : 0.581 6.399 26142 Z= 0.294 Chirality : 0.040 0.239 3032 Planarity : 0.005 0.047 3181 Dihedral : 17.726 171.958 3451 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.59 % Allowed : 20.11 % Favored : 78.30 % 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 aren not related in a simple way. whole: -1.10 (0.18), residues: 2198 helix: 0.33 (0.21), residues: 660 sheet: -0.13 (0.25), residues: 453 loop : -1.70 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 164 TYR 0.018 0.001 TYR B 40 PHE 0.036 0.001 PHE F 232 TRP 0.009 0.001 TRP B 66 HIS 0.004 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00251 (19041) covalent geometry : angle 0.58138 (26142) hydrogen bonds : bond 0.03528 ( 726) hydrogen bonds : angle 5.08895 ( 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 205 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.007 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 57 MET cc_start: 0.5631 (tpp) cc_final: 0.4403 (tpt) REVERT: A 272 ARG cc_start: 0.5796 (mtm-85) cc_final: 0.5534 (mtt180) REVERT: B 143 LYS cc_start: 0.3472 (OUTLIER) cc_final: 0.2750 (mmtt) REVERT: C 180 VAL cc_start: 0.7406 (m) cc_final: 0.7169 (m) REVERT: E 101 HIS cc_start: 0.5029 (OUTLIER) cc_final: 0.4690 (m170) REVERT: E 117 PHE cc_start: 0.7225 (t80) cc_final: 0.6948 (t80) REVERT: F 109 LEU cc_start: 0.6371 (tp) cc_final: 0.6154 (tp) REVERT: F 188 VAL cc_start: 0.4632 (m) cc_final: 0.4339 (m) REVERT: F 261 ARG cc_start: 0.6119 (ttm110) cc_final: 0.5698 (mtm-85) REVERT: G 48 MET cc_start: 0.5863 (mmt) cc_final: 0.5263 (mmt) REVERT: G 57 MET cc_start: 0.7392 (mmm) cc_final: 0.7152 (mmm) REVERT: G 68 LYS cc_start: 0.6745 (pttt) cc_final: 0.5941 (mmmt) REVERT: G 135 ARG cc_start: 0.5664 (mtt-85) cc_final: 0.5278 (mtm180) outliers start: 29 outliers final: 22 residues processed: 201 average time/residue: 0.3531 time to fit residues: 107.8167 Evaluate side-chains 191 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 ASN 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: 4.9990 chunk 26 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.186414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.152143 restraints weight = 80331.085| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.43 r_work: 0.4154 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 1.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19041 Z= 0.170 Angle : 0.644 6.630 26142 Z= 0.333 Chirality : 0.042 0.196 3032 Planarity : 0.006 0.069 3181 Dihedral : 17.821 171.805 3451 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.70 % Allowed : 20.16 % Favored : 78.13 % 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 aren not related in a simple way. whole: -1.31 (0.18), residues: 2198 helix: 0.16 (0.21), residues: 654 sheet: -0.31 (0.24), residues: 475 loop : -1.81 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 261 TYR 0.013 0.002 TYR F 314 PHE 0.016 0.002 PHE D 154 TRP 0.010 0.002 TRP B 66 HIS 0.013 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00393 (19041) covalent geometry : angle 0.64447 (26142) hydrogen bonds : bond 0.03955 ( 726) hydrogen bonds : angle 5.27641 ( 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 199 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.059 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 272 ARG cc_start: 0.5752 (mtm-85) cc_final: 0.5521 (mtt180) REVERT: E 1 MET cc_start: 0.1382 (mmm) cc_final: -0.0309 (mmt) REVERT: E 101 HIS cc_start: 0.5169 (OUTLIER) cc_final: 0.4783 (m170) REVERT: G 48 MET cc_start: 0.6054 (mmt) cc_final: 0.5381 (mmt) REVERT: G 68 LYS cc_start: 0.6779 (pttt) cc_final: 0.5955 (mmmt) REVERT: G 135 ARG cc_start: 0.5535 (mtt-85) cc_final: 0.5292 (mtm180) REVERT: G 311 ILE cc_start: 0.6757 (mm) cc_final: 0.6319 (mm) outliers start: 31 outliers final: 27 residues processed: 196 average time/residue: 0.3556 time to fit residues: 105.3951 Evaluate side-chains 187 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 126 HIS Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 55 GLN 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 274 THR Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 228 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.186966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.150581 restraints weight = 79791.346| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.74 r_work: 0.4161 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 1.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19041 Z= 0.129 Angle : 0.604 7.004 26142 Z= 0.308 Chirality : 0.041 0.200 3032 Planarity : 0.005 0.061 3181 Dihedral : 17.820 171.562 3451 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.59 % Allowed : 20.38 % Favored : 78.02 % 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 aren not related in a simple way. whole: -1.20 (0.18), residues: 2198 helix: 0.29 (0.21), residues: 653 sheet: -0.26 (0.24), residues: 475 loop : -1.75 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 164 TYR 0.014 0.001 TYR B 40 PHE 0.017 0.001 PHE D 154 TRP 0.009 0.001 TRP B 66 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00295 (19041) covalent geometry : angle 0.60358 (26142) hydrogen bonds : bond 0.03727 ( 726) hydrogen bonds : angle 5.15526 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11618.43 seconds wall clock time: 197 minutes 26.82 seconds (11846.82 seconds total)