Starting phenix.real_space_refine on Fri Jul 3 17:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ed1_47930/07_2026/9ed1_47930.map" } resolution = 3.5 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: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 K 5 8.98 5 S 108 5.16 5 C 9892 2.51 5 N 2740 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s 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: 15449 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15449 At special positions: 0 Unit cell: (138.46, 138.46, 107.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 K 5 19.00 S 108 16.00 O 2692 8.00 N 2740 7.00 C 9892 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: 1.04 Conformation dependent library (CDL) restraints added in 624.7 milliseconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.509A pdb=" N LEU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 removed outlier: 3.597A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.577A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 92 removed outlier: 3.853A pdb=" N VAL A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.105A pdb=" N ALA A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.123A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.547A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.622A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.543A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.633A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 4.127A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.873A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 289 removed outlier: 4.280A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 332 removed outlier: 3.854A pdb=" N VAL A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 369 removed outlier: 3.811A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.713A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.664A pdb=" N VAL B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.842A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.096A pdb=" N ALA B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 100' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.853A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.737A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.551A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.595A pdb=" N ARG B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 3.535A pdb=" N PHE B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 4.183A pdb=" N LEU B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.920A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 289 removed outlier: 4.259A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 315 removed outlier: 3.877A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 332 removed outlier: 4.547A pdb=" N LEU B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 369 removed outlier: 4.202A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 removed outlier: 4.221A pdb=" N HIS B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.629A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.907A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 91 removed outlier: 3.645A pdb=" N LEU C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 88 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 89 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 4.080A pdb=" N ALA C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 100' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.849A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.864A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.598A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 176 through 184 removed outlier: 4.450A pdb=" N ILE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.514A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.984A pdb=" N LEU C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.935A pdb=" N ILE C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 289 removed outlier: 3.597A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.718A pdb=" N TYR C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 369 removed outlier: 4.420A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 3.776A pdb=" N MET C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 3.898A pdb=" N LEU D 32 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 removed outlier: 3.680A pdb=" N VAL D 61 " --> pdb=" O TYR D 57 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR D 69 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 91 removed outlier: 3.723A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.045A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.622A pdb=" N ILE D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 155 removed outlier: 3.701A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.528A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.582A pdb=" N SER D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 203 through 219 removed outlier: 4.007A pdb=" N LEU D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.527A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.890A pdb=" N ILE D 246 " --> pdb=" O TRP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.769A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 315 removed outlier: 3.829A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 336 through 368 removed outlier: 3.783A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 344 " --> pdb=" O HIS D 340 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.591A pdb=" N MET D 376 " --> pdb=" O SER D 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.570A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.630A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 112 removed outlier: 3.862A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.533A pdb=" N GLY F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.909A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.707A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.777A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 Processing helix chain 'G' and resid 5 through 21 removed outlier: 3.578A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.519A pdb=" N GLY G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 removed outlier: 3.611A pdb=" N GLU G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.693A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.507A pdb=" N LEU G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 147 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 30 through 39 removed outlier: 3.651A pdb=" N THR H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.827A pdb=" N ILE H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 76 removed outlier: 3.724A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 101 through 112 removed outlier: 3.846A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 787 hydrogen bonds defined for protein. 2346 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: 2.67 Time building geometry restraints manager: 1.39 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: 5074 1.34 - 1.46: 3397 1.46 - 1.58: 7053 1.58 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15712 Sorted by residual: bond pdb=" N PRO A 119 " pdb=" CA PRO A 119 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.28e-01 bond pdb=" N PRO B 119 " pdb=" CA PRO B 119 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.08e-01 bond pdb=" CA ASP F 131 " pdb=" CB ASP F 131 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.93e-01 bond pdb=" CA ILE C 244 " pdb=" C ILE C 244 " ideal model delta sigma weight residual 1.523 1.530 -0.007 9.20e-03 1.18e+04 5.91e-01 bond pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.72e-01 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 20983 1.68 - 3.36: 223 3.36 - 5.05: 26 5.05 - 6.73: 17 6.73 - 8.41: 3 Bond angle restraints: 21252 Sorted by residual: angle pdb=" N ILE B 182 " pdb=" CA ILE B 182 " pdb=" C ILE B 182 " ideal model delta sigma weight residual 113.43 107.00 6.43 1.09e+00 8.42e-01 3.48e+01 angle pdb=" N ILE H 85 " pdb=" CA ILE H 85 " pdb=" C ILE H 85 " ideal model delta sigma weight residual 112.96 108.27 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" N MET A 46 " pdb=" CA MET A 46 " pdb=" C MET A 46 " ideal model delta sigma weight residual 113.88 108.79 5.09 1.23e+00 6.61e-01 1.71e+01 angle pdb=" N SER B 181 " pdb=" CA SER B 181 " pdb=" C SER B 181 " ideal model delta sigma weight residual 113.97 109.20 4.77 1.28e+00 6.10e-01 1.39e+01 angle pdb=" N ASN A 186 " pdb=" CA ASN A 186 " pdb=" C ASN A 186 " ideal model delta sigma weight residual 114.39 109.08 5.31 1.45e+00 4.76e-01 1.34e+01 ... (remaining 21247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8543 18.00 - 36.00: 657 36.00 - 54.00: 117 54.00 - 72.00: 7 72.00 - 90.00: 8 Dihedral angle restraints: 9332 sinusoidal: 3536 harmonic: 5796 Sorted by residual: dihedral pdb=" CA THR F 44 " pdb=" C THR F 44 " pdb=" N GLU F 45 " pdb=" CA GLU F 45 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU G 84 " pdb=" C GLU G 84 " pdb=" N ILE G 85 " pdb=" CA ILE G 85 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG D 342 " pdb=" CD ARG D 342 " pdb=" NE ARG D 342 " pdb=" CZ ARG D 342 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 9329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1573 0.030 - 0.060: 721 0.060 - 0.091: 141 0.091 - 0.121: 40 0.121 - 0.151: 5 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CB ILE A 251 " pdb=" CA ILE A 251 " pdb=" CG1 ILE A 251 " pdb=" CG2 ILE A 251 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA GLU A 321 " pdb=" N GLU A 321 " pdb=" C GLU A 321 " pdb=" CB GLU A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ASP F 131 " pdb=" N ASP F 131 " pdb=" C ASP F 131 " pdb=" CB ASP F 131 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2477 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 118 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO D 119 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 318 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C VAL A 318 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 318 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 319 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 118 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO A 119 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.015 5.00e-02 4.00e+02 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 5115 2.84 - 3.42: 15864 3.42 - 3.99: 25212 3.99 - 4.57: 37085 4.57 - 5.14: 53057 Nonbonded interactions: 136333 Sorted by model distance: nonbonded pdb=" OH TYR C 253 " pdb=" OG1 THR D 247 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU F 31 " pdb="CA CA F 201 " model vdw 2.272 3.250 nonbonded pdb=" O ARG F 106 " pdb=" OG1 THR F 110 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR G 44 " pdb=" OE1 GLU G 47 " model vdw 2.291 3.040 nonbonded pdb=" OE2 GLU G 31 " pdb="CA CA G 201 " model vdw 2.292 3.250 ... (remaining 136328 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 386) selection = (chain 'B' and resid 9 through 386) selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 11.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15712 Z= 0.096 Angle : 0.489 8.409 21252 Z= 0.277 Chirality : 0.035 0.151 2480 Planarity : 0.003 0.036 2664 Dihedral : 13.057 89.999 5580 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.17 (0.20), residues: 1996 helix: -0.50 (0.15), residues: 1456 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 359 TYR 0.010 0.001 TYR A 179 PHE 0.013 0.001 PHE H 141 TRP 0.010 0.001 TRP A 242 HIS 0.003 0.000 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.10 (15712) covalent geometry : angle 0.48851 / 0.28 (21252) hydrogen bonds : bond 0.15043 / 9.60 ( 787) hydrogen bonds : angle 4.77613 / 3.23 ( 2346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.6725 (p0) cc_final: 0.6485 (p0) REVERT: B 14 ARG cc_start: 0.7390 (ttt180) cc_final: 0.7147 (ttp80) REVERT: B 46 MET cc_start: 0.7990 (ttm) cc_final: 0.7780 (ttp) REVERT: B 255 ASP cc_start: 0.7051 (p0) cc_final: 0.6578 (p0) REVERT: C 255 ASP cc_start: 0.7029 (p0) cc_final: 0.6607 (p0) REVERT: D 217 LEU cc_start: 0.8716 (tp) cc_final: 0.8504 (tp) REVERT: D 255 ASP cc_start: 0.7089 (p0) cc_final: 0.6598 (p0) REVERT: E 7 GLU cc_start: 0.7023 (tp30) cc_final: 0.6712 (tp30) REVERT: F 24 ASP cc_start: 0.7488 (p0) cc_final: 0.7034 (p0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1171 time to fit residues: 46.0473 Evaluate side-chains 198 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.165903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141236 restraints weight = 17373.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.137880 restraints weight = 27390.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134058 restraints weight = 25798.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133471 restraints weight = 32891.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134233 restraints weight = 28071.333| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15712 Z= 0.115 Angle : 0.484 7.476 21252 Z= 0.251 Chirality : 0.037 0.145 2480 Planarity : 0.003 0.034 2664 Dihedral : 3.931 19.254 2164 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.72 % Allowed : 6.94 % Favored : 92.34 % 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 (0.20), residues: 1996 helix: -0.36 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -0.68 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 362 TYR 0.011 0.001 TYR D 326 PHE 0.013 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15712) covalent geometry : angle 0.48401 / 0.25 (21252) hydrogen bonds : bond 0.04173 / 2.67 ( 787) hydrogen bonds : angle 3.72758 / 2.61 ( 2346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: C 321 GLU cc_start: 0.8136 (mp0) cc_final: 0.7924 (mp0) REVERT: D 46 MET cc_start: 0.8125 (ttm) cc_final: 0.7896 (ttp) REVERT: D 217 LEU cc_start: 0.8827 (tp) cc_final: 0.8622 (tp) REVERT: D 255 ASP cc_start: 0.7204 (p0) cc_final: 0.6816 (p0) REVERT: E 7 GLU cc_start: 0.7329 (tp30) cc_final: 0.6971 (tp30) outliers start: 11 outliers final: 9 residues processed: 220 average time/residue: 0.1060 time to fit residues: 35.4839 Evaluate side-chains 217 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.6980 chunk 149 optimal weight: 0.0270 chunk 73 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.168127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.144141 restraints weight = 17502.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139144 restraints weight = 27649.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.137035 restraints weight = 27731.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136085 restraints weight = 25373.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135806 restraints weight = 25776.326| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15712 Z= 0.091 Angle : 0.436 6.724 21252 Z= 0.226 Chirality : 0.035 0.139 2480 Planarity : 0.002 0.033 2664 Dihedral : 3.739 17.484 2164 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.11 % Allowed : 9.62 % Favored : 89.27 % 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: -0.60 (0.20), residues: 1996 helix: -0.19 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 362 TYR 0.009 0.001 TYR D 326 PHE 0.013 0.001 PHE H 68 TRP 0.008 0.001 TRP A 242 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (15712) covalent geometry : angle 0.43643 / 0.23 (21252) hydrogen bonds : bond 0.03345 / 2.15 ( 787) hydrogen bonds : angle 3.48151 / 2.44 ( 2346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: D 255 ASP cc_start: 0.7163 (p0) cc_final: 0.6779 (p0) REVERT: E 7 GLU cc_start: 0.7257 (tp30) cc_final: 0.6891 (tp30) REVERT: F 45 GLU cc_start: 0.7010 (tp30) cc_final: 0.6765 (mm-30) REVERT: H 133 ASP cc_start: 0.6803 (p0) cc_final: 0.6597 (p0) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.0918 time to fit residues: 31.1590 Evaluate side-chains 206 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 78 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.165040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.140628 restraints weight = 17498.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135111 restraints weight = 28799.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131588 restraints weight = 28574.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130780 restraints weight = 34034.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131839 restraints weight = 27951.251| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15712 Z= 0.120 Angle : 0.464 6.540 21252 Z= 0.239 Chirality : 0.037 0.135 2480 Planarity : 0.003 0.030 2664 Dihedral : 3.869 17.266 2164 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.64 % Allowed : 10.41 % Favored : 87.96 % 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: -0.48 (0.20), residues: 1996 helix: -0.09 (0.15), residues: 1468 sheet: None (None), residues: 0 loop : -0.59 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.009 0.001 TYR D 326 PHE 0.019 0.001 PHE H 141 TRP 0.010 0.001 TRP A 242 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (15712) covalent geometry : angle 0.46441 / 0.24 (21252) hydrogen bonds : bond 0.03845 / 2.50 ( 787) hydrogen bonds : angle 3.51642 / 2.47 ( 2346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 7 GLU cc_start: 0.7329 (tp30) cc_final: 0.6961 (tp30) REVERT: E 145 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6259 (ttm) REVERT: F 45 GLU cc_start: 0.7104 (tp30) cc_final: 0.6829 (mm-30) REVERT: H 133 ASP cc_start: 0.6892 (p0) cc_final: 0.6646 (p0) outliers start: 25 outliers final: 18 residues processed: 206 average time/residue: 0.1002 time to fit residues: 32.0438 Evaluate side-chains 209 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 0.0000 chunk 103 optimal weight: 0.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 340 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.165947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140969 restraints weight = 17511.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138586 restraints weight = 28635.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137338 restraints weight = 34206.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135816 restraints weight = 32311.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135758 restraints weight = 31601.011| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15712 Z= 0.100 Angle : 0.444 7.038 21252 Z= 0.228 Chirality : 0.036 0.134 2480 Planarity : 0.002 0.029 2664 Dihedral : 3.753 16.370 2164 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.37 % Allowed : 11.32 % Favored : 87.30 % 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: -0.43 (0.20), residues: 1996 helix: -0.07 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.51 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 362 TYR 0.008 0.001 TYR D 326 PHE 0.015 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (15712) covalent geometry : angle 0.44404 / 0.23 (21252) hydrogen bonds : bond 0.03367 / 2.19 ( 787) hydrogen bonds : angle 3.40776 / 2.39 ( 2346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 145 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6058 (ttm) REVERT: F 45 GLU cc_start: 0.6978 (tp30) cc_final: 0.6775 (mm-30) REVERT: H 133 ASP cc_start: 0.6490 (p0) cc_final: 0.6218 (p0) outliers start: 21 outliers final: 16 residues processed: 205 average time/residue: 0.1014 time to fit residues: 32.3968 Evaluate side-chains 214 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 0.0070 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 129 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.165378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.140456 restraints weight = 17365.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138026 restraints weight = 27784.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136454 restraints weight = 34291.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135667 restraints weight = 31274.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135690 restraints weight = 29542.294| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15712 Z= 0.101 Angle : 0.445 8.542 21252 Z= 0.228 Chirality : 0.036 0.134 2480 Planarity : 0.002 0.029 2664 Dihedral : 3.709 15.847 2164 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.70 % Allowed : 12.04 % Favored : 86.26 % 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: -0.34 (0.20), residues: 1996 helix: -0.01 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.47 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.017 0.001 TYR C 326 PHE 0.014 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15712) covalent geometry : angle 0.44461 / 0.23 (21252) hydrogen bonds : bond 0.03359 / 2.19 ( 787) hydrogen bonds : angle 3.35915 / 2.36 ( 2346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7867 (ttm) cc_final: 0.7627 (ttp) REVERT: A 321 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: E 145 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6206 (ttm) REVERT: H 133 ASP cc_start: 0.6469 (p0) cc_final: 0.6253 (p0) outliers start: 26 outliers final: 19 residues processed: 213 average time/residue: 0.1069 time to fit residues: 34.7704 Evaluate side-chains 217 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 110 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 48 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.164767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.139619 restraints weight = 17310.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139214 restraints weight = 27670.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137838 restraints weight = 29427.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136656 restraints weight = 31102.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135970 restraints weight = 30042.207| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15712 Z= 0.101 Angle : 0.447 9.504 21252 Z= 0.227 Chirality : 0.036 0.131 2480 Planarity : 0.002 0.028 2664 Dihedral : 3.682 15.408 2164 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 12.30 % Favored : 85.73 % 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: -0.27 (0.20), residues: 1996 helix: 0.04 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 362 TYR 0.015 0.001 TYR C 326 PHE 0.015 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (15712) covalent geometry : angle 0.44716 / 0.23 (21252) hydrogen bonds : bond 0.03316 / 2.16 ( 787) hydrogen bonds : angle 3.33347 / 2.34 ( 2346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 321 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: D 303 MET cc_start: 0.7917 (mmt) cc_final: 0.7574 (mmt) REVERT: E 145 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6210 (ttm) REVERT: H 133 ASP cc_start: 0.6350 (p0) cc_final: 0.6138 (p0) REVERT: H 145 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6621 (ttp) outliers start: 30 outliers final: 21 residues processed: 213 average time/residue: 0.1069 time to fit residues: 35.1308 Evaluate side-chains 221 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.163785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.139538 restraints weight = 17551.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134105 restraints weight = 28379.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131668 restraints weight = 30318.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131401 restraints weight = 26852.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131223 restraints weight = 24500.076| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15712 Z= 0.134 Angle : 0.486 10.763 21252 Z= 0.245 Chirality : 0.037 0.129 2480 Planarity : 0.003 0.028 2664 Dihedral : 3.865 15.690 2164 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.90 % Allowed : 12.43 % Favored : 85.67 % 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: -0.29 (0.20), residues: 1996 helix: 0.05 (0.15), residues: 1468 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.015 0.001 TYR C 326 PHE 0.015 0.001 PHE H 141 TRP 0.010 0.001 TRP D 242 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 (15712) covalent geometry : angle 0.48627 / 0.25 (21252) hydrogen bonds : bond 0.03857 / 2.52 ( 787) hydrogen bonds : angle 3.44747 / 2.41 ( 2346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: E 145 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6157 (ttm) REVERT: H 133 ASP cc_start: 0.6874 (p0) cc_final: 0.6649 (p0) outliers start: 29 outliers final: 21 residues processed: 211 average time/residue: 0.1043 time to fit residues: 33.6786 Evaluate side-chains 212 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 199 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.164116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.138550 restraints weight = 17395.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135982 restraints weight = 27861.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133819 restraints weight = 35690.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133165 restraints weight = 36112.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.133044 restraints weight = 30694.015| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15712 Z= 0.113 Angle : 0.484 11.643 21252 Z= 0.242 Chirality : 0.036 0.129 2480 Planarity : 0.002 0.027 2664 Dihedral : 3.816 19.225 2164 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 12.24 % Favored : 85.67 % 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: -0.31 (0.20), residues: 1996 helix: 0.01 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.43 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 86 TYR 0.014 0.001 TYR C 326 PHE 0.013 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (15712) covalent geometry : angle 0.48406 / 0.24 (21252) hydrogen bonds : bond 0.03580 / 2.33 ( 787) hydrogen bonds : angle 3.38989 / 2.37 ( 2346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 321 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: E 145 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6113 (ttm) REVERT: H 133 ASP cc_start: 0.6662 (p0) cc_final: 0.6433 (p0) REVERT: H 145 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6675 (ttp) outliers start: 32 outliers final: 25 residues processed: 206 average time/residue: 0.1012 time to fit residues: 32.2276 Evaluate side-chains 219 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.0470 chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.164963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.139214 restraints weight = 17449.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137424 restraints weight = 27456.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135775 restraints weight = 33081.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.134258 restraints weight = 33384.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.134455 restraints weight = 32593.180| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15712 Z= 0.108 Angle : 0.486 12.751 21252 Z= 0.241 Chirality : 0.036 0.131 2480 Planarity : 0.002 0.028 2664 Dihedral : 3.780 22.762 2164 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.09 % Allowed : 12.24 % Favored : 85.67 % 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: -0.26 (0.20), residues: 1996 helix: 0.04 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 362 TYR 0.014 0.001 TYR C 326 PHE 0.013 0.001 PHE H 141 TRP 0.009 0.001 TRP A 242 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15712) covalent geometry : angle 0.48638 / 0.24 (21252) hydrogen bonds : bond 0.03452 / 2.25 ( 787) hydrogen bonds : angle 3.35086 / 2.35 ( 2346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: E 145 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6060 (ttm) REVERT: H 133 ASP cc_start: 0.6534 (p0) cc_final: 0.6313 (p0) REVERT: H 145 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6635 (ttp) outliers start: 32 outliers final: 26 residues processed: 210 average time/residue: 0.1049 time to fit residues: 34.0307 Evaluate side-chains 220 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 3 optimal weight: 0.0870 chunk 193 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.166585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141720 restraints weight = 17302.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139493 restraints weight = 28546.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.137936 restraints weight = 34319.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136509 restraints weight = 31368.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.136066 restraints weight = 30549.430| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15712 Z= 0.089 Angle : 0.469 12.644 21252 Z= 0.232 Chirality : 0.035 0.129 2480 Planarity : 0.002 0.027 2664 Dihedral : 3.616 23.363 2164 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.83 % Allowed : 12.57 % Favored : 85.60 % 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: -0.11 (0.20), residues: 1996 helix: 0.15 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.013 0.001 TYR C 326 PHE 0.013 0.001 PHE H 141 TRP 0.009 0.001 TRP D 242 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (15712) covalent geometry : angle 0.46898 / 0.23 (21252) hydrogen bonds : bond 0.02994 / 1.95 ( 787) hydrogen bonds : angle 3.22529 / 2.26 ( 2346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.81 seconds wall clock time: 41 minutes 57.91 seconds (2517.91 seconds total)