Starting phenix.real_space_refine on Sat Jul 4 07:53:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.map" model { file = "/net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ylx_73096/07_2026/9ylx_73096.cif" } resolution = 2.45 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 88 5.16 5 C 11913 2.51 5 N 3386 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18958 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2317 Classifications: {'peptide': 292} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 275} Chain: "B" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2325 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 276} Chain: "C" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2332 Classifications: {'peptide': 295} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2331 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 278} Chain: "F" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2332 Classifications: {'peptide': 295} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2317 Classifications: {'peptide': 292} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 275} Chain: "H" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2317 Classifications: {'peptide': 292} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 275} Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "J" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 3} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "L" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Time building chain proxies: 4.43, per 1000 atoms: 0.23 Number of scatterers: 18958 At special positions: 0 Unit cell: (119.004, 132.508, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 16 15.00 O 3555 8.00 N 3386 7.00 C 11913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 802.8 milliseconds 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 29 sheets defined 41.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.602A pdb=" N LEU A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.011A pdb=" N GLN A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.581A pdb=" N ARG A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.648A pdb=" N LEU B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.090A pdb=" N GLN B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.611A pdb=" N ARG B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.730A pdb=" N GLU B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 removed outlier: 5.909A pdb=" N ASN C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.518A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 94 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.552A pdb=" N MET C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.889A pdb=" N GLN C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 241 through 257 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'D' and resid 3 through 15 removed outlier: 5.775A pdb=" N ASN D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.510A pdb=" N THR D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.824A pdb=" N GLN D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 216 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'E' and resid 3 through 15 removed outlier: 6.030A pdb=" N ASN E 10 " --> pdb=" O ARG E 6 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.571A pdb=" N TYR E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 Processing helix chain 'E' and resid 153 through 161 Processing helix chain 'E' and resid 177 through 189 Processing helix chain 'E' and resid 210 through 221 removed outlier: 3.741A pdb=" N GLN E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 216 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 218 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'F' and resid 3 through 15 removed outlier: 5.741A pdb=" N ASN F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TYR F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 removed outlier: 3.589A pdb=" N THR F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 79 through 94 Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 177 through 189 Processing helix chain 'F' and resid 210 through 221 removed outlier: 3.916A pdb=" N GLN F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 216 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE F 217 " --> pdb=" O GLU F 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 283 through 296 Processing helix chain 'G' and resid 4 through 15 removed outlier: 5.520A pdb=" N ASN G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.710A pdb=" N TYR G 71 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 95 Processing helix chain 'G' and resid 153 through 161 Processing helix chain 'G' and resid 177 through 189 Processing helix chain 'G' and resid 210 through 221 removed outlier: 4.136A pdb=" N GLN G 214 " --> pdb=" O SER G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.573A pdb=" N ARG G 230 " --> pdb=" O PRO G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'H' and resid 4 through 15 removed outlier: 5.835A pdb=" N ASN H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.672A pdb=" N PHE H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 161 removed outlier: 3.636A pdb=" N MET H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 189 Processing helix chain 'H' and resid 210 through 221 removed outlier: 4.096A pdb=" N GLN H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 removed outlier: 3.707A pdb=" N ARG H 230 " --> pdb=" O PRO H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 283 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.557A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 196 removed outlier: 6.742A pdb=" N ARG A 167 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 196 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 169 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE A 235 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 168 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN A 237 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 170 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS A 261 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG A 266 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL A 277 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.669A pdb=" N ASP B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 196 removed outlier: 6.664A pdb=" N ARG B 167 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU B 196 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 169 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS B 261 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG B 266 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL B 277 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 24 Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 191 through 196 removed outlier: 7.120A pdb=" N ARG C 167 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU C 196 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 169 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE C 235 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 168 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN C 237 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 170 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 261 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG C 266 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL C 277 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AB6, first strand: chain 'D' and resid 191 through 196 removed outlier: 7.011A pdb=" N ARG D 167 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU D 196 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 169 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE D 235 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D 168 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN D 237 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 170 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS D 261 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG D 266 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL D 277 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.537A pdb=" N ASP E 22 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AC1, first strand: chain 'E' and resid 191 through 196 removed outlier: 7.182A pdb=" N ARG E 167 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU E 196 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL E 169 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE E 235 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE E 168 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN E 237 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 170 " --> pdb=" O ASN E 237 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS E 261 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 262 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL E 280 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG E 264 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 21 through 24 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AC4, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AC5, first strand: chain 'F' and resid 191 through 196 removed outlier: 7.166A pdb=" N ARG F 167 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LEU F 196 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL F 169 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE F 235 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE F 168 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN F 237 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU F 170 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS F 261 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG F 266 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL F 277 " --> pdb=" O ARG F 266 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 21 through 24 Processing sheet with id=AC7, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.537A pdb=" N ASP G 148 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 191 through 196 removed outlier: 6.742A pdb=" N ARG G 167 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU G 196 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 169 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS G 261 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG G 266 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL G 277 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 21 through 24 Processing sheet with id=AD1, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.531A pdb=" N ARG H 145 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP H 148 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 191 through 196 removed outlier: 6.602A pdb=" N ARG H 167 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU H 196 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL H 169 " --> pdb=" O LEU H 196 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE H 235 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE H 168 " --> pdb=" O ILE H 235 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN H 237 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 170 " --> pdb=" O ASN H 237 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS H 261 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG H 266 " --> pdb=" O VAL H 277 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL H 277 " --> pdb=" O ARG H 266 " (cutoff:3.500A) 803 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6353 1.34 - 1.46: 3408 1.46 - 1.58: 9397 1.58 - 1.69: 28 1.69 - 1.81: 152 Bond restraints: 19338 Sorted by residual: bond pdb=" N PRO A 175 " pdb=" CA PRO A 175 " ideal model delta sigma weight residual 1.467 1.503 -0.037 1.17e-02 7.31e+03 9.75e+00 bond pdb=" C GLN A 174 " pdb=" N PRO A 175 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N ILE A 184 " pdb=" CA ILE A 184 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.63e+00 bond pdb=" N ASN A 180 " pdb=" CA ASN A 180 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.75e+00 ... (remaining 19333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 25918 1.85 - 3.70: 305 3.70 - 5.55: 27 5.55 - 7.40: 4 7.40 - 9.25: 3 Bond angle restraints: 26257 Sorted by residual: angle pdb=" C3' A L 2 " pdb=" O3' A L 2 " pdb=" P A L 3 " ideal model delta sigma weight residual 120.20 126.16 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA THR A 177 " pdb=" CB THR A 177 " pdb=" OG1 THR A 177 " ideal model delta sigma weight residual 109.60 104.48 5.12 1.50e+00 4.44e-01 1.16e+01 angle pdb=" C GLN E 253 " pdb=" CA GLN E 253 " pdb=" CB GLN E 253 " ideal model delta sigma weight residual 110.79 105.57 5.22 1.66e+00 3.63e-01 9.91e+00 angle pdb=" C4' A L 2 " pdb=" C3' A L 2 " pdb=" O3' A L 2 " ideal model delta sigma weight residual 109.40 114.10 -4.70 1.50e+00 4.44e-01 9.82e+00 angle pdb=" O3' A L 2 " pdb=" P A L 3 " pdb=" OP1 A L 3 " ideal model delta sigma weight residual 108.00 117.25 -9.25 3.00e+00 1.11e-01 9.50e+00 ... (remaining 26252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 11140 29.60 - 59.20: 618 59.20 - 88.81: 42 88.81 - 118.41: 5 118.41 - 148.01: 2 Dihedral angle restraints: 11807 sinusoidal: 5072 harmonic: 6735 Sorted by residual: dihedral pdb=" O4' A I 4 " pdb=" C1' A I 4 " pdb=" N9 A I 4 " pdb=" C4 A I 4 " ideal model delta sinusoidal sigma weight residual 68.00 141.94 -73.94 1 1.70e+01 3.46e-03 2.40e+01 dihedral pdb=" CA ASP F 125 " pdb=" C ASP F 125 " pdb=" N CYS F 126 " pdb=" CA CYS F 126 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" O4' A K 4 " pdb=" C1' A K 4 " pdb=" N9 A K 4 " pdb=" C4 A K 4 " ideal model delta sinusoidal sigma weight residual 68.00 135.21 -67.21 1 1.70e+01 3.46e-03 2.03e+01 ... (remaining 11804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2190 0.042 - 0.084: 465 0.084 - 0.126: 306 0.126 - 0.168: 21 0.168 - 0.210: 3 Chirality restraints: 2985 Sorted by residual: chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' A L 2 " pdb=" C4' A L 2 " pdb=" O3' A L 2 " pdb=" C2' A L 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" P A L 3 " pdb=" OP1 A L 3 " pdb=" OP2 A L 3 " pdb=" O5' A L 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.59 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 2982 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 96 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO H 97 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " 0.216 9.50e-02 1.11e+02 9.71e-02 5.78e+00 pdb=" NE ARG A 181 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A L 1 " 0.023 2.00e-02 2.50e+03 1.01e-02 2.82e+00 pdb=" N9 A L 1 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A L 1 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A L 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A L 1 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A L 1 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A L 1 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A L 1 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A L 1 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A L 1 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A L 1 " -0.003 2.00e-02 2.50e+03 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4341 2.81 - 3.33: 16171 3.33 - 3.85: 30817 3.85 - 4.38: 37165 4.38 - 4.90: 63346 Nonbonded interactions: 151840 Sorted by model distance: nonbonded pdb=" CB SER F 65 " pdb=" OD2 ASP F 70 " model vdw 2.283 3.440 nonbonded pdb=" NE2 GLN C 253 " pdb=" OE1 GLN E 253 " model vdw 2.320 3.120 nonbonded pdb=" OG SER C 294 " pdb=" NH1 ARG E 230 " model vdw 2.348 3.120 nonbonded pdb=" O ASP F 70 " pdb=" OD1 ASP F 70 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP F 69 " pdb=" CB CYS F 111 " model vdw 2.510 3.440 ... (remaining 151835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'B' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'C' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'D' and resid 3 through 294) selection = (chain 'E' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'F' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'G' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) selection = (chain 'H' and (resid 3 through 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 through 294)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.630 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.770 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.002 0.037 19338 Z= 0.138 Angle : 0.499 9.246 26257 Z= 0.291 Chirality : 0.046 0.210 2985 Planarity : 0.005 0.097 3346 Dihedral : 16.699 148.009 7469 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.10 % Allowed : 17.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2333 helix: 1.85 (0.18), residues: 860 sheet: 1.16 (0.28), residues: 358 loop : -0.32 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 100 TYR 0.013 0.001 TYR D 71 PHE 0.008 0.001 PHE G 36 TRP 0.015 0.001 TRP E 5 HIS 0.001 0.000 HIS E 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (19338) covalent geometry : angle 0.49881 / 0.29 (26257) hydrogen bonds : bond 0.12163 / 8.03 ( 803) hydrogen bonds : angle 5.69525 / 4.07 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.805 Fit side-chains REVERT: A 25 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7859 (ttt-90) REVERT: A 289 LYS cc_start: 0.7253 (mttt) cc_final: 0.6911 (mtpm) REVERT: B 258 ARG cc_start: 0.7685 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: C 129 GLU cc_start: 0.8106 (tt0) cc_final: 0.7825 (tt0) REVERT: C 213 GLU cc_start: 0.8426 (mp0) cc_final: 0.8170 (mm-30) REVERT: D 61 LYS cc_start: 0.8296 (mppt) cc_final: 0.8004 (mmtm) REVERT: D 62 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 289 LYS cc_start: 0.8587 (mttt) cc_final: 0.8303 (mtmt) REVERT: E 16 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: E 58 ILE cc_start: 0.8307 (mt) cc_final: 0.8052 (mt) REVERT: E 289 LYS cc_start: 0.8502 (mttt) cc_final: 0.8114 (mtmp) REVERT: F 125 ASP cc_start: 0.7708 (m-30) cc_final: 0.7301 (m-30) REVERT: G 81 ASP cc_start: 0.6492 (t70) cc_final: 0.6118 (p0) REVERT: G 88 ASN cc_start: 0.7131 (m110) cc_final: 0.6593 (m-40) REVERT: G 104 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6512 (mm-30) REVERT: G 165 ASP cc_start: 0.7641 (p0) cc_final: 0.7262 (p0) REVERT: G 227 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7145 (mp0) REVERT: G 287 ARG cc_start: 0.8064 (ttt90) cc_final: 0.7593 (ttt-90) REVERT: G 289 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7435 (tttm) REVERT: H 47 ILE cc_start: 0.7299 (mt) cc_final: 0.7069 (tt) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.8752 time to fit residues: 291.6909 Evaluate side-chains 287 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 ASN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121497 restraints weight = 18618.067| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.26 r_work: 0.3179 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19338 Z= 0.167 Angle : 0.556 9.557 26257 Z= 0.292 Chirality : 0.049 0.303 2985 Planarity : 0.005 0.061 3346 Dihedral : 9.170 147.942 2777 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.24 % Allowed : 15.85 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2333 helix: 1.98 (0.18), residues: 864 sheet: 1.03 (0.27), residues: 358 loop : -0.41 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.024 0.002 TYR A 71 PHE 0.010 0.002 PHE H 172 TRP 0.014 0.002 TRP F 5 HIS 0.003 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (19338) covalent geometry : angle 0.55585 / 0.29 (26257) hydrogen bonds : bond 0.04972 / 3.30 ( 803) hydrogen bonds : angle 4.71819 / 3.31 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 0.828 Fit side-chains REVERT: A 25 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7732 (ttt-90) REVERT: A 289 LYS cc_start: 0.7095 (mttt) cc_final: 0.6696 (mtpm) REVERT: B 26 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: B 258 ARG cc_start: 0.7658 (ptt-90) cc_final: 0.7175 (ptt-90) REVERT: C 102 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: C 125 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: C 129 GLU cc_start: 0.8100 (tt0) cc_final: 0.7820 (tt0) REVERT: C 213 GLU cc_start: 0.8424 (mp0) cc_final: 0.8154 (mm-30) REVERT: C 253 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: D 61 LYS cc_start: 0.8262 (mppt) cc_final: 0.7978 (mmtm) REVERT: D 138 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7565 (p) REVERT: D 141 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6418 (mmt) REVERT: D 191 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7041 (ttp-170) REVERT: D 253 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: D 289 LYS cc_start: 0.8573 (mttt) cc_final: 0.8229 (mtmt) REVERT: E 16 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8213 (mtt-85) REVERT: E 26 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: E 167 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7369 (tpp80) REVERT: E 289 LYS cc_start: 0.8541 (mttt) cc_final: 0.7909 (mmtt) REVERT: F 6 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7801 (ttm-80) REVERT: F 26 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: F 125 ASP cc_start: 0.8033 (m-30) cc_final: 0.7555 (m-30) REVERT: G 35 LYS cc_start: 0.6927 (mtpp) cc_final: 0.6484 (mttp) REVERT: G 55 ILE cc_start: 0.4472 (OUTLIER) cc_final: 0.4166 (mm) REVERT: G 81 ASP cc_start: 0.6579 (t70) cc_final: 0.6141 (p0) REVERT: G 88 ASN cc_start: 0.7063 (m110) cc_final: 0.6514 (m-40) REVERT: G 104 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6254 (mm-30) REVERT: G 133 ASP cc_start: 0.7023 (m-30) cc_final: 0.6637 (t0) REVERT: G 165 ASP cc_start: 0.7571 (p0) cc_final: 0.7124 (p0) REVERT: G 189 ASN cc_start: 0.7964 (t0) cc_final: 0.7586 (m-40) REVERT: G 287 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7363 (ttt-90) REVERT: G 289 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7281 (tttm) REVERT: H 148 ASP cc_start: 0.7542 (m-30) cc_final: 0.7281 (m-30) REVERT: H 191 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6494 (ttm170) outliers start: 66 outliers final: 21 residues processed: 330 average time/residue: 0.8688 time to fit residues: 313.0344 Evaluate side-chains 322 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 191 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122959 restraints weight = 18794.234| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.05 r_work: 0.3191 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19338 Z= 0.129 Angle : 0.506 9.075 26257 Z= 0.267 Chirality : 0.047 0.217 2985 Planarity : 0.005 0.070 3346 Dihedral : 9.175 150.757 2777 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.94 % Allowed : 16.83 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2333 helix: 2.15 (0.18), residues: 864 sheet: 1.00 (0.27), residues: 358 loop : -0.39 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 258 TYR 0.019 0.001 TYR A 71 PHE 0.008 0.001 PHE H 172 TRP 0.014 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19338) covalent geometry : angle 0.50593 / 0.27 (26257) hydrogen bonds : bond 0.04245 / 2.80 ( 803) hydrogen bonds : angle 4.55155 / 3.18 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7817 (ttt-90) REVERT: A 289 LYS cc_start: 0.7141 (mttt) cc_final: 0.6769 (mtpm) REVERT: B 26 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6581 (pp20) REVERT: C 102 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: C 129 GLU cc_start: 0.8102 (tt0) cc_final: 0.7822 (tt0) REVERT: C 213 GLU cc_start: 0.8462 (mp0) cc_final: 0.8201 (mm-30) REVERT: C 253 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: D 61 LYS cc_start: 0.8327 (mppt) cc_final: 0.8029 (mmtm) REVERT: D 138 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7582 (p) REVERT: D 141 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6463 (mmt) REVERT: D 191 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7101 (ttp-170) REVERT: D 253 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: D 289 LYS cc_start: 0.8568 (mttt) cc_final: 0.8256 (mtmt) REVERT: E 16 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8258 (mtt-85) REVERT: E 26 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: E 289 LYS cc_start: 0.8531 (mttt) cc_final: 0.7981 (mmtt) REVERT: F 6 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7834 (ttm-80) REVERT: F 26 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: F 125 ASP cc_start: 0.7994 (m-30) cc_final: 0.7533 (m-30) REVERT: G 35 LYS cc_start: 0.7031 (mtpp) cc_final: 0.6582 (mttp) REVERT: G 55 ILE cc_start: 0.4567 (OUTLIER) cc_final: 0.4254 (mm) REVERT: G 81 ASP cc_start: 0.6577 (t70) cc_final: 0.6158 (p0) REVERT: G 88 ASN cc_start: 0.7125 (m110) cc_final: 0.6573 (m-40) REVERT: G 104 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6341 (mm-30) REVERT: G 133 ASP cc_start: 0.7133 (m-30) cc_final: 0.6733 (t0) REVERT: G 165 ASP cc_start: 0.7625 (p0) cc_final: 0.7201 (p0) REVERT: G 287 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7414 (ttt-90) REVERT: G 289 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7286 (tttm) REVERT: H 148 ASP cc_start: 0.7584 (m-30) cc_final: 0.7345 (m-30) outliers start: 60 outliers final: 28 residues processed: 325 average time/residue: 0.8382 time to fit residues: 297.9687 Evaluate side-chains 329 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 11 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 89 GLN F 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115772 restraints weight = 18738.048| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.79 r_work: 0.3168 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19338 Z= 0.250 Angle : 0.648 9.385 26257 Z= 0.341 Chirality : 0.053 0.437 2985 Planarity : 0.006 0.082 3346 Dihedral : 9.464 152.247 2777 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.48 % Allowed : 16.78 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2333 helix: 1.76 (0.18), residues: 864 sheet: 0.72 (0.27), residues: 366 loop : -0.50 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 255 TYR 0.024 0.002 TYR A 71 PHE 0.012 0.002 PHE H 172 TRP 0.016 0.002 TRP F 5 HIS 0.004 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.25 (19338) covalent geometry : angle 0.64784 / 0.34 (26257) hydrogen bonds : bond 0.05952 / 3.94 ( 803) hydrogen bonds : angle 4.73034 / 3.31 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7821 (ttt-90) REVERT: A 289 LYS cc_start: 0.7336 (mttt) cc_final: 0.6949 (mtpm) REVERT: B 26 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: B 100 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7497 (ttt90) REVERT: B 258 ARG cc_start: 0.7672 (ptt-90) cc_final: 0.7209 (ptt-90) REVERT: C 102 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: C 129 GLU cc_start: 0.8083 (tt0) cc_final: 0.7796 (tt0) REVERT: C 213 GLU cc_start: 0.8441 (mp0) cc_final: 0.8179 (mm-30) REVERT: C 253 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 61 LYS cc_start: 0.8363 (mppt) cc_final: 0.8051 (mmtm) REVERT: D 141 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6519 (mmt) REVERT: D 191 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7093 (ttp-170) REVERT: D 253 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: D 289 LYS cc_start: 0.8604 (mttt) cc_final: 0.8281 (mtmt) REVERT: E 16 ARG cc_start: 0.8463 (mtt-85) cc_final: 0.8235 (mtt-85) REVERT: E 26 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: E 253 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: E 289 LYS cc_start: 0.8569 (mttt) cc_final: 0.7993 (mmtt) REVERT: F 6 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: F 26 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: G 35 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6621 (mttp) REVERT: G 55 ILE cc_start: 0.4437 (OUTLIER) cc_final: 0.4050 (mm) REVERT: G 81 ASP cc_start: 0.6583 (t70) cc_final: 0.6160 (p0) REVERT: G 88 ASN cc_start: 0.7090 (m110) cc_final: 0.6529 (m-40) REVERT: G 104 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6398 (mm-30) REVERT: G 133 ASP cc_start: 0.7178 (m-30) cc_final: 0.6783 (t0) REVERT: G 165 ASP cc_start: 0.7660 (p0) cc_final: 0.7207 (p0) REVERT: G 179 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7937 (tt) REVERT: G 189 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7580 (m-40) REVERT: G 287 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7413 (ttt-90) REVERT: G 289 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7325 (tttm) REVERT: H 148 ASP cc_start: 0.7618 (m-30) cc_final: 0.7386 (m-30) REVERT: H 191 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6654 (ttm170) outliers start: 71 outliers final: 30 residues processed: 330 average time/residue: 0.8633 time to fit residues: 310.9308 Evaluate side-chains 331 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 191 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 162 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 185 optimal weight: 0.0040 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 261 HIS B 189 ASN F 89 GLN F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120818 restraints weight = 18798.227| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.82 r_work: 0.3237 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19338 Z= 0.098 Angle : 0.474 9.438 26257 Z= 0.252 Chirality : 0.046 0.222 2985 Planarity : 0.004 0.082 3346 Dihedral : 9.306 155.003 2777 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.06 % Allowed : 18.65 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2333 helix: 2.22 (0.18), residues: 864 sheet: 1.09 (0.27), residues: 352 loop : -0.42 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.015 0.001 TYR F 71 PHE 0.008 0.001 PHE G 36 TRP 0.015 0.001 TRP E 5 HIS 0.002 0.001 HIS F 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (19338) covalent geometry : angle 0.47410 / 0.25 (26257) hydrogen bonds : bond 0.03537 / 2.31 ( 803) hydrogen bonds : angle 4.40254 / 3.08 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.778 Fit side-chains REVERT: A 25 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7791 (ttt-90) REVERT: A 289 LYS cc_start: 0.7119 (mttt) cc_final: 0.6751 (mtpm) REVERT: B 26 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6479 (pp20) REVERT: C 102 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: C 129 GLU cc_start: 0.8036 (tt0) cc_final: 0.7749 (tt0) REVERT: C 213 GLU cc_start: 0.8425 (mp0) cc_final: 0.8162 (mm-30) REVERT: C 253 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: D 61 LYS cc_start: 0.8339 (mppt) cc_final: 0.8018 (mmtm) REVERT: D 138 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7581 (p) REVERT: D 141 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6506 (mmt) REVERT: D 191 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7056 (ttp-170) REVERT: D 253 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: D 289 LYS cc_start: 0.8519 (mttt) cc_final: 0.8207 (mtmt) REVERT: E 16 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8221 (mtt-85) REVERT: E 167 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7104 (tpp80) REVERT: E 253 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8323 (tm130) REVERT: E 289 LYS cc_start: 0.8476 (mttt) cc_final: 0.7938 (mmtt) REVERT: F 26 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: F 125 ASP cc_start: 0.7898 (m-30) cc_final: 0.7481 (m-30) REVERT: F 285 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8017 (t70) REVERT: G 35 LYS cc_start: 0.6995 (mtpp) cc_final: 0.6503 (mttp) REVERT: G 55 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.4144 (mm) REVERT: G 81 ASP cc_start: 0.6571 (t70) cc_final: 0.6171 (p0) REVERT: G 88 ASN cc_start: 0.7147 (m110) cc_final: 0.6602 (m-40) REVERT: G 104 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6308 (mm-30) REVERT: G 106 MET cc_start: 0.7046 (ptm) cc_final: 0.6618 (ptm) REVERT: G 133 ASP cc_start: 0.7146 (m-30) cc_final: 0.6739 (t0) REVERT: G 165 ASP cc_start: 0.7630 (p0) cc_final: 0.7224 (p0) REVERT: G 287 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7387 (ttt-90) REVERT: G 289 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7302 (tttm) REVERT: H 148 ASP cc_start: 0.7582 (m-30) cc_final: 0.7331 (m-30) outliers start: 42 outliers final: 16 residues processed: 313 average time/residue: 0.8746 time to fit residues: 299.1110 Evaluate side-chains 320 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 218 optimal weight: 0.2980 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 178 GLN F 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118157 restraints weight = 18619.588| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.78 r_work: 0.3202 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19338 Z= 0.172 Angle : 0.549 9.031 26257 Z= 0.290 Chirality : 0.049 0.297 2985 Planarity : 0.005 0.087 3346 Dihedral : 9.302 152.803 2777 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.85 % Allowed : 17.76 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2333 helix: 2.10 (0.18), residues: 864 sheet: 0.94 (0.27), residues: 358 loop : -0.47 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 258 TYR 0.021 0.002 TYR A 71 PHE 0.010 0.002 PHE H 172 TRP 0.013 0.001 TRP F 5 HIS 0.003 0.001 HIS E 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (19338) covalent geometry : angle 0.54880 / 0.29 (26257) hydrogen bonds : bond 0.04653 / 3.08 ( 803) hydrogen bonds : angle 4.48998 / 3.14 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7798 (ttt-90) REVERT: A 289 LYS cc_start: 0.7204 (mttt) cc_final: 0.6816 (mtpm) REVERT: B 26 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6688 (pp20) REVERT: B 258 ARG cc_start: 0.7624 (ptt-90) cc_final: 0.7186 (ptt-90) REVERT: C 102 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: C 129 GLU cc_start: 0.8047 (tt0) cc_final: 0.7762 (tt0) REVERT: C 213 GLU cc_start: 0.8426 (mp0) cc_final: 0.8159 (mm-30) REVERT: C 253 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: D 61 LYS cc_start: 0.8344 (mppt) cc_final: 0.8022 (mmtm) REVERT: D 138 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7588 (p) REVERT: D 141 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6473 (mmt) REVERT: D 191 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7068 (ttp-170) REVERT: D 253 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: D 289 LYS cc_start: 0.8564 (mttt) cc_final: 0.8266 (mtmt) REVERT: E 16 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.8230 (mtt-85) REVERT: E 26 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: E 167 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7695 (tpp80) REVERT: E 253 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: E 289 LYS cc_start: 0.8537 (mttt) cc_final: 0.7975 (mmtt) REVERT: F 6 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7769 (ttm-80) REVERT: F 26 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: F 125 ASP cc_start: 0.8131 (m-30) cc_final: 0.7722 (m-30) REVERT: F 235 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (mt) REVERT: F 285 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8022 (t70) REVERT: G 35 LYS cc_start: 0.7060 (mtpp) cc_final: 0.6559 (mttp) REVERT: G 55 ILE cc_start: 0.4488 (OUTLIER) cc_final: 0.4118 (mm) REVERT: G 81 ASP cc_start: 0.6561 (t70) cc_final: 0.6161 (p0) REVERT: G 88 ASN cc_start: 0.7149 (m110) cc_final: 0.6590 (m-40) REVERT: G 104 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6344 (mm-30) REVERT: G 133 ASP cc_start: 0.7153 (m-30) cc_final: 0.6772 (t0) REVERT: G 165 ASP cc_start: 0.7631 (p0) cc_final: 0.7220 (p0) REVERT: G 287 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7395 (ttt-90) REVERT: G 289 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7320 (tttm) REVERT: H 29 MET cc_start: 0.4206 (tpt) cc_final: 0.3988 (mmm) REVERT: H 148 ASP cc_start: 0.7570 (m-30) cc_final: 0.7340 (m-30) outliers start: 58 outliers final: 27 residues processed: 327 average time/residue: 0.8517 time to fit residues: 303.9757 Evaluate side-chains 332 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 292 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 146 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119841 restraints weight = 18680.378| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.24 r_work: 0.3140 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19338 Z= 0.248 Angle : 0.645 9.238 26257 Z= 0.340 Chirality : 0.053 0.421 2985 Planarity : 0.006 0.095 3346 Dihedral : 9.527 154.418 2777 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.24 % Allowed : 17.62 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2333 helix: 1.77 (0.17), residues: 864 sheet: 0.67 (0.27), residues: 366 loop : -0.52 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 258 TYR 0.024 0.002 TYR A 71 PHE 0.011 0.002 PHE H 172 TRP 0.015 0.002 TRP F 5 HIS 0.004 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.25 (19338) covalent geometry : angle 0.64504 / 0.34 (26257) hydrogen bonds : bond 0.05828 / 3.86 ( 803) hydrogen bonds : angle 4.66842 / 3.26 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7769 (ttt-90) REVERT: A 289 LYS cc_start: 0.7243 (mttt) cc_final: 0.6837 (mtpm) REVERT: B 26 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: B 258 ARG cc_start: 0.7653 (ptt-90) cc_final: 0.7181 (ptt-90) REVERT: C 102 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: C 129 GLU cc_start: 0.8149 (tt0) cc_final: 0.7869 (tt0) REVERT: C 213 GLU cc_start: 0.8470 (mp0) cc_final: 0.8200 (mm-30) REVERT: C 253 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: D 61 LYS cc_start: 0.8354 (mppt) cc_final: 0.8024 (mmtm) REVERT: D 141 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6482 (mmt) REVERT: D 191 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7090 (ttp-170) REVERT: D 253 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: D 289 LYS cc_start: 0.8608 (mttt) cc_final: 0.8218 (mtmt) REVERT: E 16 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8215 (mtt-85) REVERT: E 26 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: E 167 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7908 (tpp80) REVERT: E 253 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: E 289 LYS cc_start: 0.8578 (mttt) cc_final: 0.7950 (mmtt) REVERT: F 6 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7820 (ttm-80) REVERT: F 26 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: F 102 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: F 125 ASP cc_start: 0.8315 (m-30) cc_final: 0.7875 (m-30) REVERT: F 253 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8398 (tm130) REVERT: G 35 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6555 (mttp) REVERT: G 81 ASP cc_start: 0.6525 (t70) cc_final: 0.6104 (p0) REVERT: G 88 ASN cc_start: 0.7059 (m110) cc_final: 0.6513 (m-40) REVERT: G 104 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6362 (mm-30) REVERT: G 133 ASP cc_start: 0.7153 (m-30) cc_final: 0.6741 (t0) REVERT: G 165 ASP cc_start: 0.7690 (p0) cc_final: 0.7214 (p0) REVERT: G 179 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8233 (tp) REVERT: G 189 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7578 (m-40) REVERT: G 287 ARG cc_start: 0.7960 (ttt90) cc_final: 0.7375 (ttt-90) REVERT: G 289 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7243 (tttm) REVERT: H 29 MET cc_start: 0.4374 (OUTLIER) cc_final: 0.4054 (mmm) REVERT: H 148 ASP cc_start: 0.7571 (m-30) cc_final: 0.7322 (m-30) outliers start: 66 outliers final: 32 residues processed: 326 average time/residue: 0.8333 time to fit residues: 296.5096 Evaluate side-chains 336 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 292 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 165 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 178 GLN B 284 GLN F 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120763 restraints weight = 18704.013| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.78 r_work: 0.3229 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19338 Z= 0.102 Angle : 0.485 9.193 26257 Z= 0.258 Chirality : 0.046 0.222 2985 Planarity : 0.005 0.088 3346 Dihedral : 9.383 156.755 2777 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.82 % Allowed : 18.99 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2333 helix: 2.20 (0.18), residues: 864 sheet: 1.03 (0.27), residues: 352 loop : -0.46 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 100 TYR 0.015 0.001 TYR F 71 PHE 0.008 0.001 PHE G 36 TRP 0.016 0.001 TRP E 5 HIS 0.002 0.001 HIS F 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (19338) covalent geometry : angle 0.48522 / 0.26 (26257) hydrogen bonds : bond 0.03615 / 2.37 ( 803) hydrogen bonds : angle 4.40559 / 3.08 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.773 Fit side-chains REVERT: A 25 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7820 (ttt-90) REVERT: A 289 LYS cc_start: 0.7170 (mttt) cc_final: 0.6782 (mtpm) REVERT: B 26 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6507 (pp20) REVERT: B 258 ARG cc_start: 0.7686 (ptt-90) cc_final: 0.7263 (ptt-90) REVERT: C 102 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: C 129 GLU cc_start: 0.8040 (tt0) cc_final: 0.7751 (tt0) REVERT: C 213 GLU cc_start: 0.8440 (mp0) cc_final: 0.8180 (mm-30) REVERT: C 253 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: D 61 LYS cc_start: 0.8346 (mppt) cc_final: 0.7983 (mmtm) REVERT: D 62 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 84 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.6977 (m) REVERT: D 138 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7589 (p) REVERT: D 141 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6547 (mmt) REVERT: D 191 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7048 (ttp-170) REVERT: D 253 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: D 289 LYS cc_start: 0.8546 (mttt) cc_final: 0.8241 (mtmt) REVERT: E 16 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.8206 (mtt-85) REVERT: E 167 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7094 (tpp80) REVERT: E 253 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8320 (tm130) REVERT: E 289 LYS cc_start: 0.8480 (mttt) cc_final: 0.8048 (mtmp) REVERT: F 26 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: F 125 ASP cc_start: 0.7934 (m-30) cc_final: 0.7533 (m-30) REVERT: F 285 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8003 (t70) REVERT: G 35 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6574 (mttp) REVERT: G 81 ASP cc_start: 0.6516 (t70) cc_final: 0.6182 (p0) REVERT: G 88 ASN cc_start: 0.7106 (m110) cc_final: 0.6559 (m-40) REVERT: G 104 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6369 (mm-30) REVERT: G 106 MET cc_start: 0.7057 (ptm) cc_final: 0.6590 (ptm) REVERT: G 133 ASP cc_start: 0.7149 (m-30) cc_final: 0.6783 (t0) REVERT: G 165 ASP cc_start: 0.7636 (p0) cc_final: 0.7237 (p0) REVERT: G 287 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7433 (ttt-90) REVERT: G 289 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7280 (tttm) REVERT: H 148 ASP cc_start: 0.7564 (m-30) cc_final: 0.7329 (m-30) outliers start: 37 outliers final: 15 residues processed: 318 average time/residue: 0.8712 time to fit residues: 302.7751 Evaluate side-chains 320 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 178 GLN C 89 GLN F 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121535 restraints weight = 18659.088| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.18 r_work: 0.3182 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19338 Z= 0.139 Angle : 0.526 10.620 26257 Z= 0.277 Chirality : 0.048 0.246 2985 Planarity : 0.005 0.091 3346 Dihedral : 9.301 153.658 2777 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.26 % Allowed : 18.74 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2333 helix: 2.20 (0.18), residues: 864 sheet: 0.94 (0.27), residues: 358 loop : -0.47 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.018 0.001 TYR A 71 PHE 0.009 0.001 PHE H 172 TRP 0.014 0.001 TRP E 5 HIS 0.003 0.001 HIS E 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (19338) covalent geometry : angle 0.52574 / 0.28 (26257) hydrogen bonds : bond 0.04216 / 2.78 ( 803) hydrogen bonds : angle 4.43825 / 3.10 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7785 (ttt-90) REVERT: A 289 LYS cc_start: 0.7150 (mttt) cc_final: 0.6756 (mtpm) REVERT: B 26 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6636 (pp20) REVERT: B 258 ARG cc_start: 0.7650 (ptt-90) cc_final: 0.7211 (ptt-90) REVERT: C 102 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: C 129 GLU cc_start: 0.8100 (tt0) cc_final: 0.7820 (tt0) REVERT: C 213 GLU cc_start: 0.8460 (mp0) cc_final: 0.8192 (mm-30) REVERT: C 253 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: D 61 LYS cc_start: 0.8330 (mppt) cc_final: 0.7956 (mmtm) REVERT: D 62 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7316 (mm-30) REVERT: D 138 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7565 (p) REVERT: D 141 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6460 (mmt) REVERT: D 191 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7058 (ttp-170) REVERT: D 253 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: D 289 LYS cc_start: 0.8585 (mttt) cc_final: 0.8253 (mtmt) REVERT: E 16 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8222 (mtt-85) REVERT: E 24 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7929 (mptp) REVERT: E 167 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7605 (tpp80) REVERT: E 289 LYS cc_start: 0.8519 (mttt) cc_final: 0.7944 (mmtt) REVERT: F 6 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7796 (ttm-80) REVERT: F 26 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: F 125 ASP cc_start: 0.8092 (m-30) cc_final: 0.7682 (m-30) REVERT: F 285 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8061 (t70) REVERT: G 35 LYS cc_start: 0.7086 (mtpp) cc_final: 0.6592 (mttp) REVERT: G 81 ASP cc_start: 0.6463 (t70) cc_final: 0.6133 (p0) REVERT: G 88 ASN cc_start: 0.7086 (m110) cc_final: 0.6538 (m-40) REVERT: G 104 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6349 (mm-30) REVERT: G 133 ASP cc_start: 0.7149 (m-30) cc_final: 0.6757 (t0) REVERT: G 165 ASP cc_start: 0.7623 (p0) cc_final: 0.7200 (p0) REVERT: G 287 ARG cc_start: 0.7874 (ttt90) cc_final: 0.7431 (ttt-90) REVERT: G 289 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7260 (tttm) REVERT: H 148 ASP cc_start: 0.7552 (m-30) cc_final: 0.7296 (m-30) outliers start: 46 outliers final: 19 residues processed: 318 average time/residue: 0.8813 time to fit residues: 305.6375 Evaluate side-chains 318 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 141 MET Chi-restraints excluded: chain H residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 178 GLN F 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120239 restraints weight = 18642.867| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.93 r_work: 0.3225 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19338 Z= 0.110 Angle : 0.492 10.190 26257 Z= 0.259 Chirality : 0.046 0.209 2985 Planarity : 0.005 0.089 3346 Dihedral : 9.236 154.450 2777 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.47 % Allowed : 19.43 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2333 helix: 2.33 (0.18), residues: 864 sheet: 1.00 (0.27), residues: 358 loop : -0.44 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 100 TYR 0.017 0.001 TYR F 71 PHE 0.007 0.001 PHE G 36 TRP 0.015 0.001 TRP E 5 HIS 0.002 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19338) covalent geometry : angle 0.49182 / 0.26 (26257) hydrogen bonds : bond 0.03679 / 2.42 ( 803) hydrogen bonds : angle 4.36695 / 3.05 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.771 Fit side-chains REVERT: A 25 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7790 (ttt-90) REVERT: A 289 LYS cc_start: 0.7098 (mttt) cc_final: 0.6728 (mtpm) REVERT: B 26 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6525 (pp20) REVERT: B 258 ARG cc_start: 0.7644 (ptt-90) cc_final: 0.7225 (ptt-90) REVERT: C 102 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: C 129 GLU cc_start: 0.7996 (tt0) cc_final: 0.7706 (tt0) REVERT: C 213 GLU cc_start: 0.8414 (mp0) cc_final: 0.8145 (mm-30) REVERT: C 253 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: D 61 LYS cc_start: 0.8325 (mppt) cc_final: 0.7945 (mmtm) REVERT: D 62 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7321 (mm-30) REVERT: D 84 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.6932 (m) REVERT: D 138 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7595 (p) REVERT: D 141 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6474 (mmt) REVERT: D 191 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7014 (ttp-170) REVERT: D 253 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: D 289 LYS cc_start: 0.8541 (mttt) cc_final: 0.8218 (mtmt) REVERT: E 16 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.8205 (mtt-85) REVERT: E 167 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7334 (tpp80) REVERT: E 289 LYS cc_start: 0.8475 (mttt) cc_final: 0.7916 (mmtt) REVERT: F 26 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: F 70 ASP cc_start: 0.7830 (t0) cc_final: 0.7570 (m-30) REVERT: F 125 ASP cc_start: 0.7920 (m-30) cc_final: 0.7518 (m-30) REVERT: F 285 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7982 (t70) REVERT: G 35 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6598 (mttp) REVERT: G 81 ASP cc_start: 0.6477 (t70) cc_final: 0.6159 (p0) REVERT: G 88 ASN cc_start: 0.7108 (m110) cc_final: 0.6561 (m-40) REVERT: G 104 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6357 (mm-30) REVERT: G 106 MET cc_start: 0.7055 (ptm) cc_final: 0.6585 (ptm) REVERT: G 133 ASP cc_start: 0.7177 (m-30) cc_final: 0.6791 (t0) REVERT: G 165 ASP cc_start: 0.7606 (p0) cc_final: 0.7209 (p0) REVERT: G 287 ARG cc_start: 0.7826 (ttt90) cc_final: 0.7384 (ttt-90) REVERT: G 289 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7277 (tttm) REVERT: H 148 ASP cc_start: 0.7553 (m-30) cc_final: 0.7299 (m-30) outliers start: 30 outliers final: 14 residues processed: 306 average time/residue: 0.8599 time to fit residues: 286.7961 Evaluate side-chains 312 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 287 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 253 GLN Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 136 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 178 GLN F 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123077 restraints weight = 18707.155| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19338 Z= 0.115 Angle : 0.498 10.730 26257 Z= 0.262 Chirality : 0.047 0.207 2985 Planarity : 0.005 0.086 3346 Dihedral : 9.180 153.588 2777 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.42 % Allowed : 19.77 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2333 helix: 2.33 (0.18), residues: 864 sheet: 1.04 (0.27), residues: 358 loop : -0.43 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 100 TYR 0.017 0.001 TYR A 71 PHE 0.008 0.001 PHE H 172 TRP 0.014 0.001 TRP E 5 HIS 0.002 0.001 HIS E 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19338) covalent geometry : angle 0.49841 / 0.26 (26257) hydrogen bonds : bond 0.03768 / 2.49 ( 803) hydrogen bonds : angle 4.36011 / 3.05 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9429.63 seconds wall clock time: 160 minutes 52.90 seconds (9652.90 seconds total)