Starting phenix.real_space_refine on Fri Jul 3 05:10:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpt_74533/07_2026/9zpt_74533.map" } resolution = 3.39 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= 1.000 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 K 4 8.98 5 S 76 5.16 5 C 7716 2.51 5 N 2176 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 12016 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2612 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2612 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 392 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 392 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 392 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 392 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 2.96, per 1000 atoms: 0.25 Number of scatterers: 12016 At special positions: 0 Unit cell: (139.32, 139.32, 97.18, 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) K 4 19.00 S 76 16.00 O 2044 8.00 N 2176 7.00 C 7716 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: 1.01 Conformation dependent library (CDL) restraints added in 621.7 milliseconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3016 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 4.117A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.723A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.656A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 4.059A pdb=" N LYS A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.715A pdb=" N ALA A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.627A pdb=" N LEU A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 159 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 161 through 171 removed outlier: 4.027A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.763A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.530A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.963A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.508A pdb=" N SER A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.887A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 262 through 289 removed outlier: 4.243A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS A 277 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 331 removed outlier: 3.925A pdb=" N VAL A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 366 removed outlier: 3.541A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.787A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.782A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.549A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 103 through 115 removed outlier: 4.010A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.551A pdb=" N LEU B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 159 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 162 " --> pdb=" O ARG B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 162' Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.703A pdb=" N LEU B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.762A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.539A pdb=" N SER B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 removed outlier: 5.209A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 265 through 289 removed outlier: 3.766A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 331 removed outlier: 3.820A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 366 Processing helix chain 'C' and resid 10 through 32 removed outlier: 4.111A pdb=" N ARG C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 50 removed outlier: 3.771A pdb=" N ILE C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.660A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 91 removed outlier: 4.072A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 86 " --> pdb=" O LYS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.967A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.629A pdb=" N LEU C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 161 through 171 removed outlier: 4.021A pdb=" N ARG C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.777A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 197 " --> pdb=" O TRP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.520A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.894A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 removed outlier: 3.506A pdb=" N SER C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 removed outlier: 4.902A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 262 through 289 removed outlier: 4.240A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS C 277 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 331 removed outlier: 3.961A pdb=" N VAL C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 366 Processing helix chain 'D' and resid 10 through 32 removed outlier: 3.789A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 removed outlier: 3.783A pdb=" N ILE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 removed outlier: 3.562A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.038A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 155 through 162 removed outlier: 3.780A pdb=" N ARG D 159 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 162 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 removed outlier: 3.706A pdb=" N LEU D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 191 through 203 removed outlier: 3.749A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS D 197 " --> pdb=" O TRP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.539A pdb=" N SER D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 5.213A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 262 through 289 removed outlier: 4.269A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N CYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 281 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 331 removed outlier: 3.816A pdb=" N VAL D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 366 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 120 through 129 removed outlier: 3.828A pdb=" N MET E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 4.496A pdb=" N MET E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 removed outlier: 3.528A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 120 through 129 removed outlier: 3.958A pdb=" N MET F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 removed outlier: 3.545A pdb=" N GLU F 140 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 120 through 129 removed outlier: 3.828A pdb=" N MET G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 4.039A pdb=" N MET G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 120 through 129 removed outlier: 3.843A pdb=" N MET H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 removed outlier: 4.455A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3966 1.34 - 1.46: 2763 1.46 - 1.58: 5383 1.58 - 1.70: 0 1.70 - 1.81: 124 Bond restraints: 12236 Sorted by residual: bond pdb=" CB LYS A 309 " pdb=" CG LYS A 309 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.99e-01 bond pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" CB LYS C 309 " pdb=" CG LYS C 309 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CA LEU A 174 " pdb=" CB LEU A 174 " ideal model delta sigma weight residual 1.527 1.548 -0.020 2.48e-02 1.63e+03 6.72e-01 bond pdb=" CB GLU E 84 " pdb=" CG GLU E 84 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.68e-01 ... (remaining 12231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 16427 2.32 - 4.64: 177 4.64 - 6.97: 16 6.97 - 9.29: 0 9.29 - 11.61: 2 Bond angle restraints: 16622 Sorted by residual: angle pdb=" N ILE C 76 " pdb=" CA ILE C 76 " pdb=" C ILE C 76 " ideal model delta sigma weight residual 111.81 107.91 3.90 8.60e-01 1.35e+00 2.05e+01 angle pdb=" N ILE A 76 " pdb=" CA ILE A 76 " pdb=" C ILE A 76 " ideal model delta sigma weight residual 111.81 107.96 3.85 8.60e-01 1.35e+00 2.01e+01 angle pdb=" N ILE D 76 " pdb=" CA ILE D 76 " pdb=" C ILE D 76 " ideal model delta sigma weight residual 111.81 108.10 3.71 8.60e-01 1.35e+00 1.87e+01 angle pdb=" N ILE B 76 " pdb=" CA ILE B 76 " pdb=" C ILE B 76 " ideal model delta sigma weight residual 111.81 108.12 3.69 8.60e-01 1.35e+00 1.84e+01 angle pdb=" CA LEU C 174 " pdb=" CB LEU C 174 " pdb=" CG LEU C 174 " ideal model delta sigma weight residual 116.30 127.91 -11.61 3.50e+00 8.16e-02 1.10e+01 ... (remaining 16617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6533 17.83 - 35.65: 520 35.65 - 53.48: 101 53.48 - 71.31: 15 71.31 - 89.14: 5 Dihedral angle restraints: 7174 sinusoidal: 2518 harmonic: 4656 Sorted by residual: dihedral pdb=" CG ARG A 352 " pdb=" CD ARG A 352 " pdb=" NE ARG A 352 " pdb=" CZ ARG A 352 " ideal model delta sinusoidal sigma weight residual 90.00 130.91 -40.91 2 1.50e+01 4.44e-03 9.15e+00 dihedral pdb=" CG ARG C 352 " pdb=" CD ARG C 352 " pdb=" NE ARG C 352 " pdb=" CZ ARG C 352 " ideal model delta sinusoidal sigma weight residual 90.00 130.89 -40.89 2 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CG ARG B 352 " pdb=" CD ARG B 352 " pdb=" NE ARG B 352 " pdb=" CZ ARG B 352 " ideal model delta sinusoidal sigma weight residual 90.00 130.89 -40.89 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 7171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1201 0.032 - 0.064: 653 0.064 - 0.096: 104 0.096 - 0.128: 22 0.128 - 0.161: 4 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CB ILE G 85 " pdb=" CA ILE G 85 " pdb=" CG1 ILE G 85 " pdb=" CG2 ILE G 85 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CB THR H 146 " pdb=" CA THR H 146 " pdb=" OG1 THR H 146 " pdb=" CG2 THR H 146 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CB THR E 146 " pdb=" CA THR E 146 " pdb=" OG1 THR E 146 " pdb=" CG2 THR E 146 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1981 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 288 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C LYS B 288 " -0.021 2.00e-02 2.50e+03 pdb=" O LYS B 288 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 289 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 288 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C LYS D 288 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS D 288 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU D 289 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 288 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C LYS C 288 " -0.018 2.00e-02 2.50e+03 pdb=" O LYS C 288 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU C 289 " 0.006 2.00e-02 2.50e+03 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 3779 2.84 - 3.41: 12579 3.41 - 3.99: 19392 3.99 - 4.56: 28011 4.56 - 5.14: 39717 Nonbonded interactions: 103478 Sorted by model distance: nonbonded pdb=" NE2 HIS B 80 " pdb=" OE2 GLU B 111 " model vdw 2.262 3.120 nonbonded pdb=" NE2 HIS D 80 " pdb=" OE2 GLU D 111 " model vdw 2.263 3.120 nonbonded pdb=" OE2 GLU C 111 " pdb=" NH2 ARG C 165 " model vdw 2.311 3.120 nonbonded pdb=" OE2 GLU A 111 " pdb=" NH2 ARG A 165 " model vdw 2.318 3.120 nonbonded pdb=" O LEU D 60 " pdb=" OG1 THR D 64 " model vdw 2.350 3.040 ... (remaining 103473 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 9 through 329 or (resid 330 and (name N or name CA or name \ C or name O or name CB )) or resid 331 through 366)) selection = (chain 'B' and (resid 9 through 326 or (resid 327 and (name N or name CA or name \ C or name O or name CB )) or resid 328 through 366)) selection = (chain 'C' and (resid 9 through 329 or (resid 330 and (name N or name CA or name \ C or name O or name CB )) or resid 331 through 366)) selection = (chain 'D' and (resid 9 through 326 or (resid 327 and (name N or name CA or name \ C or name O or name CB )) or resid 328 through 366)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 10.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.250 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12236 Z= 0.134 Angle : 0.619 11.610 16622 Z= 0.356 Chirality : 0.037 0.161 1984 Planarity : 0.003 0.027 2074 Dihedral : 13.863 89.136 4158 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.21), residues: 1604 helix: -0.71 (0.16), residues: 1196 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 359 TYR 0.006 0.001 TYR A 199 PHE 0.014 0.001 PHE B 248 TRP 0.015 0.001 TRP C 96 HIS 0.003 0.000 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (12236) covalent geometry : angle 0.61884 / 0.36 (16622) hydrogen bonds : bond 0.17771 / 11.91 ( 673) hydrogen bonds : angle 5.71628 / 4.14 ( 1989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.472 Fit side-chains REVERT: B 56 LEU cc_start: 0.7568 (mm) cc_final: 0.7213 (tt) REVERT: B 320 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 320 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 56 LEU cc_start: 0.7658 (mm) cc_final: 0.7264 (tt) REVERT: D 309 LYS cc_start: 0.8422 (tttm) cc_final: 0.8077 (tmtt) REVERT: D 320 GLN cc_start: 0.7497 (tm-30) cc_final: 0.6947 (tm-30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1155 time to fit residues: 25.7381 Evaluate side-chains 144 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS C 43 HIS E 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.226070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180892 restraints weight = 12920.505| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.51 r_work: 0.3415 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12236 Z= 0.144 Angle : 0.542 7.705 16622 Z= 0.275 Chirality : 0.036 0.115 1984 Planarity : 0.003 0.028 2074 Dihedral : 4.216 17.394 1734 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.45 % Allowed : 7.91 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1604 helix: -0.24 (0.16), residues: 1160 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 359 TYR 0.007 0.001 TYR A 253 PHE 0.012 0.001 PHE C 248 TRP 0.016 0.001 TRP A 96 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (12236) covalent geometry : angle 0.54222 / 0.28 (16622) hydrogen bonds : bond 0.04617 / 3.10 ( 673) hydrogen bonds : angle 3.83350 / 2.72 ( 1989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.440 Fit side-chains REVERT: B 56 LEU cc_start: 0.8015 (mm) cc_final: 0.7497 (tt) REVERT: C 306 GLN cc_start: 0.7905 (tp40) cc_final: 0.7705 (mm110) REVERT: C 320 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 45 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 56 LEU cc_start: 0.8070 (mm) cc_final: 0.7521 (tt) outliers start: 5 outliers final: 3 residues processed: 143 average time/residue: 0.1154 time to fit residues: 23.7654 Evaluate side-chains 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain D residue 46 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 117 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS F 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.224358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.187181 restraints weight = 12920.490| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.63 r_work: 0.3514 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12236 Z= 0.160 Angle : 0.546 7.081 16622 Z= 0.279 Chirality : 0.036 0.117 1984 Planarity : 0.003 0.029 2074 Dihedral : 4.290 20.497 1734 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.62 % Allowed : 10.34 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1604 helix: -0.12 (0.16), residues: 1164 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 359 TYR 0.008 0.001 TYR C 253 PHE 0.013 0.001 PHE A 248 TRP 0.014 0.001 TRP D 242 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (12236) covalent geometry : angle 0.54558 / 0.28 (16622) hydrogen bonds : bond 0.04697 / 3.15 ( 673) hydrogen bonds : angle 3.73059 / 2.65 ( 1989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.7912 (mm) cc_final: 0.7467 (tt) REVERT: C 320 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7505 (tm-30) REVERT: D 56 LEU cc_start: 0.8010 (mm) cc_final: 0.7519 (tt) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.1120 time to fit residues: 23.8728 Evaluate side-chains 145 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 102 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.225801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186786 restraints weight = 12939.961| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.76 r_work: 0.3505 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12236 Z= 0.130 Angle : 0.520 7.555 16622 Z= 0.264 Chirality : 0.035 0.112 1984 Planarity : 0.003 0.030 2074 Dihedral : 4.129 20.600 1734 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.62 % Allowed : 12.05 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1604 helix: 0.00 (0.16), residues: 1164 sheet: None (None), residues: 0 loop : -1.61 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 359 TYR 0.006 0.001 TYR C 253 PHE 0.012 0.001 PHE C 248 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12236) covalent geometry : angle 0.52040 / 0.26 (16622) hydrogen bonds : bond 0.04218 / 2.83 ( 673) hydrogen bonds : angle 3.54521 / 2.52 ( 1989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.7891 (mm) cc_final: 0.7412 (tt) REVERT: C 320 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 56 LEU cc_start: 0.7959 (mm) cc_final: 0.7453 (tt) outliers start: 18 outliers final: 13 residues processed: 156 average time/residue: 0.1156 time to fit residues: 25.9649 Evaluate side-chains 148 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 115 optimal weight: 0.0070 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.225268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.192396 restraints weight = 12997.995| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.96 r_work: 0.3963 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12236 Z= 0.134 Angle : 0.530 8.118 16622 Z= 0.268 Chirality : 0.035 0.112 1984 Planarity : 0.003 0.028 2074 Dihedral : 4.127 20.957 1734 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 12.95 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1604 helix: -0.07 (0.16), residues: 1208 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 359 TYR 0.006 0.001 TYR D 253 PHE 0.011 0.001 PHE A 248 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (12236) covalent geometry : angle 0.53018 / 0.27 (16622) hydrogen bonds : bond 0.04212 / 2.82 ( 673) hydrogen bonds : angle 3.52740 / 2.51 ( 1989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.7567 (mm) cc_final: 0.7302 (tt) REVERT: C 320 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 344 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8125 (tp) REVERT: D 45 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7732 (mm-30) REVERT: D 56 LEU cc_start: 0.7660 (mm) cc_final: 0.7336 (tt) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.1089 time to fit residues: 24.5529 Evaluate side-chains 154 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.0010 chunk 131 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.228230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194395 restraints weight = 12904.515| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.09 r_work: 0.4023 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12236 Z= 0.103 Angle : 0.501 8.898 16622 Z= 0.252 Chirality : 0.033 0.104 1984 Planarity : 0.003 0.029 2074 Dihedral : 3.836 17.605 1734 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.80 % Allowed : 13.40 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1604 helix: 0.18 (0.17), residues: 1176 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 359 TYR 0.003 0.001 TYR D 326 PHE 0.010 0.001 PHE C 248 TRP 0.009 0.001 TRP D 242 HIS 0.002 0.000 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (12236) covalent geometry : angle 0.50082 / 0.25 (16622) hydrogen bonds : bond 0.03564 / 2.39 ( 673) hydrogen bonds : angle 3.31217 / 2.35 ( 1989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 46 MET cc_start: 0.7934 (tmm) cc_final: 0.7467 (ttp) REVERT: B 56 LEU cc_start: 0.7547 (mm) cc_final: 0.7291 (tt) REVERT: C 320 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 344 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8134 (tp) REVERT: D 56 LEU cc_start: 0.7661 (mm) cc_final: 0.7321 (tt) REVERT: D 313 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7295 (mp0) outliers start: 20 outliers final: 15 residues processed: 161 average time/residue: 0.1010 time to fit residues: 23.8417 Evaluate side-chains 160 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 23 optimal weight: 0.0050 chunk 159 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.228417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182079 restraints weight = 12889.025| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 4.68 r_work: 0.3434 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12236 Z= 0.103 Angle : 0.505 9.292 16622 Z= 0.253 Chirality : 0.033 0.106 1984 Planarity : 0.002 0.026 2074 Dihedral : 3.748 15.899 1734 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1604 helix: 0.22 (0.16), residues: 1196 sheet: None (None), residues: 0 loop : -1.96 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 359 TYR 0.004 0.001 TYR D 253 PHE 0.010 0.001 PHE A 248 TRP 0.010 0.001 TRP D 242 HIS 0.003 0.000 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (12236) covalent geometry : angle 0.50480 / 0.25 (16622) hydrogen bonds : bond 0.03510 / 2.35 ( 673) hydrogen bonds : angle 3.24839 / 2.30 ( 1989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: B 46 MET cc_start: 0.8062 (tmm) cc_final: 0.7732 (ttp) REVERT: B 56 LEU cc_start: 0.7908 (mm) cc_final: 0.7414 (tt) REVERT: C 320 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 344 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8129 (tp) REVERT: D 56 LEU cc_start: 0.8076 (mm) cc_final: 0.7474 (tt) REVERT: D 313 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.0965 time to fit residues: 22.6992 Evaluate side-chains 156 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.222657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.213993 restraints weight = 12984.232| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 0.61 r_work: 0.4315 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12236 Z= 0.199 Angle : 0.601 9.404 16622 Z= 0.303 Chirality : 0.038 0.127 1984 Planarity : 0.003 0.035 2074 Dihedral : 4.320 23.687 1734 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.43 % Allowed : 13.31 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1604 helix: -0.01 (0.16), residues: 1208 sheet: None (None), residues: 0 loop : -2.00 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.007 0.001 TYR B 253 PHE 0.014 0.001 PHE B 248 TRP 0.016 0.002 TRP D 242 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 (12236) covalent geometry : angle 0.60120 / 0.30 (16622) hydrogen bonds : bond 0.04875 / 3.27 ( 673) hydrogen bonds : angle 3.62512 / 2.58 ( 1989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 46 MET cc_start: 0.7578 (tmm) cc_final: 0.7102 (ttp) REVERT: C 320 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 344 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7970 (tp) REVERT: D 46 MET cc_start: 0.7699 (tmm) cc_final: 0.7233 (ttp) REVERT: D 313 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6452 (mp0) outliers start: 27 outliers final: 21 residues processed: 157 average time/residue: 0.1076 time to fit residues: 24.6891 Evaluate side-chains 162 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.225213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.176708 restraints weight = 12882.662| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.97 r_work: 0.3372 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12236 Z= 0.136 Angle : 0.572 12.390 16622 Z= 0.281 Chirality : 0.035 0.113 1984 Planarity : 0.003 0.030 2074 Dihedral : 4.077 21.944 1734 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.98 % Allowed : 14.21 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1604 helix: 0.08 (0.16), residues: 1208 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.005 0.001 TYR D 253 PHE 0.011 0.001 PHE C 248 TRP 0.012 0.001 TRP D 242 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (12236) covalent geometry : angle 0.57197 / 0.28 (16622) hydrogen bonds : bond 0.04138 / 2.77 ( 673) hydrogen bonds : angle 3.45945 / 2.45 ( 1989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.450 Fit side-chains REVERT: B 46 MET cc_start: 0.8118 (tmm) cc_final: 0.7788 (ttp) REVERT: C 320 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 344 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8142 (tp) REVERT: D 46 MET cc_start: 0.8241 (tmm) cc_final: 0.7925 (ttp) REVERT: D 313 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7579 (mp0) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.1079 time to fit residues: 23.8992 Evaluate side-chains 153 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 41 optimal weight: 1.9990 chunk 156 optimal weight: 0.0670 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.225779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.216773 restraints weight = 12970.643| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 0.64 r_work: 0.4336 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.4301 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12236 Z= 0.128 Angle : 0.563 10.905 16622 Z= 0.278 Chirality : 0.035 0.110 1984 Planarity : 0.003 0.028 2074 Dihedral : 3.975 20.273 1734 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.62 % Allowed : 14.66 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.22), residues: 1604 helix: 0.14 (0.16), residues: 1208 sheet: None (None), residues: 0 loop : -1.92 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.005 0.001 TYR D 253 PHE 0.011 0.001 PHE D 248 TRP 0.012 0.001 TRP D 242 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12236) covalent geometry : angle 0.56286 / 0.28 (16622) hydrogen bonds : bond 0.03976 / 2.66 ( 673) hydrogen bonds : angle 3.40676 / 2.41 ( 1989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.459 Fit side-chains REVERT: A 344 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7770 (tp) REVERT: B 46 MET cc_start: 0.7525 (tmm) cc_final: 0.7072 (ttp) REVERT: C 320 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 344 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7936 (tp) REVERT: D 313 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6394 (mp0) outliers start: 18 outliers final: 15 residues processed: 150 average time/residue: 0.1093 time to fit residues: 23.9553 Evaluate side-chains 156 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 157 optimal weight: 0.0070 chunk 145 optimal weight: 20.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.223227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.214078 restraints weight = 12959.055| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 0.63 r_work: 0.4317 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.4286 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12236 Z= 0.168 Angle : 0.603 10.339 16622 Z= 0.300 Chirality : 0.036 0.120 1984 Planarity : 0.003 0.030 2074 Dihedral : 4.232 23.232 1734 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.89 % Allowed : 14.57 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1604 helix: 0.08 (0.16), residues: 1208 sheet: None (None), residues: 0 loop : -1.97 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.007 0.001 TYR D 253 PHE 0.013 0.001 PHE A 248 TRP 0.015 0.002 TRP D 242 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (12236) covalent geometry : angle 0.60346 / 0.30 (16622) hydrogen bonds : bond 0.04555 / 3.05 ( 673) hydrogen bonds : angle 3.53594 / 2.51 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.52 seconds wall clock time: 50 minutes 4.20 seconds (3004.20 seconds total)