Starting phenix.real_space_refine on Thu Sep 18 14:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gj3_0010/09_2025/6gj3_0010.map" } resolution = 4.3 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 11009 2.51 5 N 3160 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17405 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 7, 'TRANS': 54} Chain breaks: 1 Chain: "D" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2473 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2482 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3509 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 29, 'TRANS': 414} Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3498 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 414} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2485 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Time building chain proxies: 4.36, per 1000 atoms: 0.25 Number of scatterers: 17405 At special positions: 0 Unit cell: (106.7, 159.5, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3156 8.00 N 3160 7.00 C 11009 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: 1.53 Conformation dependent library (CDL) restraints added in 830.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 31.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'D' and resid 15 through 35 removed outlier: 3.972A pdb=" N PHE D 19 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 32 " --> pdb=" O HIS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 218 removed outlier: 3.784A pdb=" N MET D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 removed outlier: 3.637A pdb=" N ALA D 242 " --> pdb=" O TRP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.908A pdb=" N LEU D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.372A pdb=" N LEU D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.987A pdb=" N PHE E 19 " --> pdb=" O MET E 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 194 through 218 removed outlier: 4.424A pdb=" N MET E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.611A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.547A pdb=" N LEU E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 3.660A pdb=" N ARG E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 removed outlier: 3.713A pdb=" N ASN E 297 " --> pdb=" O THR E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 297' Processing helix chain 'E' and resid 298 through 310 removed outlier: 3.573A pdb=" N ASN E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 308 " --> pdb=" O SER E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 35 removed outlier: 3.843A pdb=" N GLN F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 194 through 222 removed outlier: 4.437A pdb=" N MET F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 246 through 251 removed outlier: 3.705A pdb=" N LEU F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 3.545A pdb=" N GLU F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 298 through 310 removed outlier: 3.582A pdb=" N ASN F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 36 removed outlier: 4.351A pdb=" N GLN G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 218 removed outlier: 4.264A pdb=" N THR G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 223 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.732A pdb=" N VAL G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.630A pdb=" N LEU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 276 removed outlier: 4.410A pdb=" N LEU G 264 " --> pdb=" O HIS G 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 removed outlier: 3.503A pdb=" N ASN G 297 " --> pdb=" O THR G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 297' Processing helix chain 'G' and resid 298 through 310 Processing helix chain 'G' and resid 354 through 366 removed outlier: 4.407A pdb=" N THR G 360 " --> pdb=" O HIS G 356 " (cutoff:3.500A) Proline residue: G 363 - end of helix Processing helix chain 'G' and resid 411 through 420 removed outlier: 3.735A pdb=" N ASP G 420 " --> pdb=" O ARG G 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 35 removed outlier: 4.331A pdb=" N PHE H 19 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.105A pdb=" N MET H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG H 211 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 212 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN H 222 " --> pdb=" O MET H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 254 removed outlier: 4.037A pdb=" N SER H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Proline residue: H 248 - end of helix removed outlier: 5.335A pdb=" N GLU H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 removed outlier: 4.121A pdb=" N LEU H 264 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 Processing helix chain 'H' and resid 298 through 310 removed outlier: 3.785A pdb=" N LEU H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.940A pdb=" N ARG H 340 " --> pdb=" O ALA H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 removed outlier: 3.958A pdb=" N ARG H 416 " --> pdb=" O THR H 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.277A pdb=" N PHE I 19 " --> pdb=" O MET I 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 35 Processing helix chain 'I' and resid 51 through 56 removed outlier: 3.572A pdb=" N LEU I 54 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Proline residue: I 55 - end of helix No H-bonds generated for 'chain 'I' and resid 51 through 56' Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 194 through 220 removed outlier: 4.138A pdb=" N LEU I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU I 203 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 210 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG I 219 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 228 removed outlier: 3.740A pdb=" N ASP I 228 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 245 removed outlier: 3.900A pdb=" N SER I 235 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 254 removed outlier: 4.074A pdb=" N LEU I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 276 removed outlier: 4.093A pdb=" N LEU I 264 " --> pdb=" O HIS I 260 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 271 " --> pdb=" O GLU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 310 removed outlier: 3.559A pdb=" N LEU I 303 " --> pdb=" O PHE I 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG I 308 " --> pdb=" O SER I 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 310 " --> pdb=" O LEU I 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.327A pdb=" N ALA D 47 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG D 63 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA D 61 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 151 through 153 removed outlier: 5.588A pdb=" N LEU D 101 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 124 through 131 removed outlier: 6.211A pdb=" N VAL D 143 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 49 removed outlier: 5.195A pdb=" N VAL E 44 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG E 67 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 46 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 63 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 97 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG E 169 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 99 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 171 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 133 removed outlier: 3.777A pdb=" N GLU E 128 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.372A pdb=" N ILE F 65 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 47 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG F 63 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE F 49 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA F 61 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.796A pdb=" N SER F 141 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AB2, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 59 " --> pdb=" O CYS G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 151 through 154 removed outlier: 3.712A pdb=" N THR G 151 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 99 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS G 165 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 125 through 131 removed outlier: 5.136A pdb=" N LYS G 126 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG G 147 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU G 128 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 318 through 321 removed outlier: 3.537A pdb=" N ILE G 321 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 439 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 325 through 326 removed outlier: 3.892A pdb=" N THR G 425 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.771A pdb=" N ILE H 65 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA H 47 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG H 63 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 61 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.613A pdb=" N THR H 151 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 101 " --> pdb=" O PRO H 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 125 through 132 removed outlier: 3.508A pdb=" N VAL H 130 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 132 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 141 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 387 through 390 Processing sheet with id=AC3, first strand: chain 'I' and resid 44 through 49 removed outlier: 5.361A pdb=" N VAL I 44 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG I 67 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG I 63 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 58 through 59 Processing sheet with id=AC5, first strand: chain 'I' and resid 151 through 153 removed outlier: 3.581A pdb=" N THR I 151 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA I 102 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 97 " --> pdb=" O ARG I 169 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG I 169 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE I 99 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL I 171 " --> pdb=" O CYS I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 126 through 127 490 hydrogen bonds defined for protein. 1389 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: 2.80 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5874 1.34 - 1.46: 3141 1.46 - 1.58: 8655 1.58 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 17807 Sorted by residual: bond pdb=" C SER H 370 " pdb=" N PRO H 371 " ideal model delta sigma weight residual 1.326 1.387 -0.060 1.44e-02 4.82e+03 1.76e+01 bond pdb=" C LEU G 14 " pdb=" N MET G 15 " ideal model delta sigma weight residual 1.333 1.278 0.055 1.59e-02 3.96e+03 1.19e+01 bond pdb=" C ASN D 81 " pdb=" N LEU D 82 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.29e+00 bond pdb=" C HIS C 232 " pdb=" N PRO C 233 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.06e+00 bond pdb=" C ARG D 121 " pdb=" N PRO D 122 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.07e+00 ... (remaining 17802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 23756 3.43 - 6.87: 462 6.87 - 10.30: 47 10.30 - 13.74: 5 13.74 - 17.17: 3 Bond angle restraints: 24273 Sorted by residual: angle pdb=" C ARG G 67 " pdb=" N PHE G 68 " pdb=" CA PHE G 68 " ideal model delta sigma weight residual 120.68 131.95 -11.27 1.52e+00 4.33e-01 5.50e+01 angle pdb=" N ILE C 220 " pdb=" CA ILE C 220 " pdb=" C ILE C 220 " ideal model delta sigma weight residual 108.88 123.67 -14.79 2.16e+00 2.14e-01 4.69e+01 angle pdb=" N VAL C 324 " pdb=" CA VAL C 324 " pdb=" C VAL C 324 " ideal model delta sigma weight residual 112.17 105.71 6.46 9.50e-01 1.11e+00 4.63e+01 angle pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta sigma weight residual 122.13 134.38 -12.25 1.85e+00 2.92e-01 4.38e+01 angle pdb=" N MET G 256 " pdb=" CA MET G 256 " pdb=" C MET G 256 " ideal model delta sigma weight residual 109.81 120.98 -11.17 2.21e+00 2.05e-01 2.55e+01 ... (remaining 24268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 10130 15.02 - 30.03: 612 30.03 - 45.05: 113 45.05 - 60.07: 18 60.07 - 75.08: 4 Dihedral angle restraints: 10877 sinusoidal: 4433 harmonic: 6444 Sorted by residual: dihedral pdb=" CA ILE C 220 " pdb=" C ILE C 220 " pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta harmonic sigma weight residual -180.00 -114.89 -65.11 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" CA TRP F 162 " pdb=" C TRP F 162 " pdb=" N LEU F 163 " pdb=" CA LEU F 163 " ideal model delta harmonic sigma weight residual 180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA CYS C 310 " pdb=" C CYS C 310 " pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta harmonic sigma weight residual 180.00 127.03 52.97 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 10874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2430 0.096 - 0.192: 314 0.192 - 0.289: 12 0.289 - 0.385: 3 0.385 - 0.481: 1 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA HIS G 40 " pdb=" N HIS G 40 " pdb=" C HIS G 40 " pdb=" CB HIS G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CG LEU I 38 " pdb=" CB LEU I 38 " pdb=" CD1 LEU I 38 " pdb=" CD2 LEU I 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB VAL G 234 " pdb=" CA VAL G 234 " pdb=" CG1 VAL G 234 " pdb=" CG2 VAL G 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2757 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 220 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO C 221 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 40 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO G 41 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 299 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO I 300 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 300 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 300 " -0.042 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3437 2.78 - 3.31: 15085 3.31 - 3.84: 26299 3.84 - 4.37: 29769 4.37 - 4.90: 50884 Nonbonded interactions: 125474 Sorted by model distance: nonbonded pdb=" OG SER F 119 " pdb=" O ARG F 121 " model vdw 2.248 3.040 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.310 3.120 nonbonded pdb=" N ASP G 80 " pdb=" OD1 ASP G 80 " model vdw 2.331 3.120 nonbonded pdb=" NH1 ARG D 212 " pdb=" OE1 GLU D 247 " model vdw 2.336 3.120 nonbonded pdb=" O MET G 256 " pdb=" N TYR G 258 " model vdw 2.350 3.120 ... (remaining 125469 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 'D' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 311)) selection = (chain 'E' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) selection = (chain 'F' and (resid 1 through 221 or (resid 222 through 225 and (name N or nam \ e CA or name C or name O or name CB )) or resid 226 through 311)) selection = (chain 'I' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) } ncs_group { reference = (chain 'G' and (resid 1 through 333 or (resid 334 through 335 and (name N or nam \ e CA or name C or name O or name CB )) or resid 336 through 346 or (resid 347 an \ d (name N or name CA or name C or name O or name CB )) or resid 348 through 444) \ ) 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.008 0.077 17807 Z= 0.361 Angle : 1.187 17.170 24273 Z= 0.652 Chirality : 0.064 0.481 2760 Planarity : 0.010 0.122 3184 Dihedral : 10.340 75.082 6647 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.45 % Favored : 86.23 % Rotamer: Outliers : 0.37 % Allowed : 2.17 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.88 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.76 (0.14), residues: 2178 helix: -3.07 (0.13), residues: 681 sheet: -2.70 (0.25), residues: 330 loop : -3.43 (0.14), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 153 TYR 0.027 0.004 TYR G 427 PHE 0.029 0.003 PHE H 19 TRP 0.046 0.004 TRP G 125 HIS 0.018 0.003 HIS H 206 Details of bonding type rmsd covalent geometry : bond 0.00823 (17807) covalent geometry : angle 1.18730 (24273) hydrogen bonds : bond 0.21860 ( 486) hydrogen bonds : angle 8.03884 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 356 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7649 (ttm170) REVERT: C 224 THR cc_start: 0.8284 (p) cc_final: 0.8073 (p) REVERT: C 319 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6350 (mm) REVERT: C 325 MET cc_start: 0.5595 (mmt) cc_final: 0.5303 (mmt) REVERT: D 237 PHE cc_start: 0.7946 (p90) cc_final: 0.7627 (t80) REVERT: D 238 TRP cc_start: 0.6927 (m100) cc_final: 0.6404 (m100) REVERT: D 251 LYS cc_start: 0.9063 (tttt) cc_final: 0.8659 (ttpt) REVERT: E 292 HIS cc_start: 0.4961 (t-90) cc_final: 0.4660 (t70) REVERT: F 198 MET cc_start: 0.8192 (mmm) cc_final: 0.7835 (mmt) REVERT: G 120 GLU cc_start: 0.7703 (pm20) cc_final: 0.7324 (pp20) REVERT: G 154 MET cc_start: 0.7808 (ttp) cc_final: 0.7468 (ttp) REVERT: G 367 LYS cc_start: 0.6536 (mttt) cc_final: 0.6135 (mtpt) REVERT: G 397 ILE cc_start: 0.5455 (mt) cc_final: 0.4936 (mt) REVERT: H 2 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7801 (mmmm) REVERT: H 4 TYR cc_start: 0.8529 (m-10) cc_final: 0.7852 (m-10) REVERT: H 67 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7473 (mmm-85) REVERT: H 188 LEU cc_start: 0.9336 (mt) cc_final: 0.9088 (mt) REVERT: H 419 LEU cc_start: 0.8829 (mt) cc_final: 0.8325 (pp) REVERT: I 138 HIS cc_start: 0.8189 (p-80) cc_final: 0.7835 (p-80) REVERT: I 258 TYR cc_start: 0.7017 (p90) cc_final: 0.6369 (p90) REVERT: I 277 THR cc_start: 0.9123 (p) cc_final: 0.8864 (t) outliers start: 7 outliers final: 3 residues processed: 362 average time/residue: 0.1644 time to fit residues: 85.4248 Evaluate side-chains 197 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 HIS ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 40 HIS F 291 HIS F 292 HIS G 156 HIS G 157 GLN H 206 HIS ** H 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 HIS I 241 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.080978 restraints weight = 48572.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083117 restraints weight = 29905.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084582 restraints weight = 21100.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085580 restraints weight = 16433.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086266 restraints weight = 13743.678| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17807 Z= 0.150 Angle : 0.756 14.098 24273 Z= 0.388 Chirality : 0.046 0.321 2760 Planarity : 0.007 0.119 3184 Dihedral : 7.575 59.609 2401 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.16), residues: 2178 helix: -1.45 (0.18), residues: 686 sheet: -2.14 (0.26), residues: 347 loop : -3.11 (0.15), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 259 TYR 0.014 0.002 TYR H 427 PHE 0.020 0.002 PHE H 426 TRP 0.024 0.002 TRP I 162 HIS 0.010 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00330 (17807) covalent geometry : angle 0.75594 (24273) hydrogen bonds : bond 0.04970 ( 486) hydrogen bonds : angle 5.75534 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5733 (mmt) cc_final: 0.5185 (mmt) REVERT: D 238 TRP cc_start: 0.7069 (m100) cc_final: 0.5987 (m100) REVERT: D 251 LYS cc_start: 0.8829 (tttt) cc_final: 0.8545 (ttpt) REVERT: E 128 GLU cc_start: 0.8205 (tp30) cc_final: 0.7985 (tt0) REVERT: E 292 HIS cc_start: 0.5197 (t-90) cc_final: 0.4756 (t70) REVERT: F 184 PHE cc_start: 0.8456 (t80) cc_final: 0.8218 (t80) REVERT: G 120 GLU cc_start: 0.7633 (pm20) cc_final: 0.7275 (pp20) REVERT: G 154 MET cc_start: 0.7758 (ttp) cc_final: 0.7410 (ttp) REVERT: G 367 LYS cc_start: 0.6482 (mttt) cc_final: 0.6206 (mtpt) REVERT: G 397 ILE cc_start: 0.5875 (mt) cc_final: 0.5503 (mt) REVERT: H 2 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8136 (mmmm) REVERT: H 4 TYR cc_start: 0.8238 (m-10) cc_final: 0.7992 (m-80) REVERT: H 419 LEU cc_start: 0.8826 (mt) cc_final: 0.8346 (pp) REVERT: I 138 HIS cc_start: 0.8051 (p-80) cc_final: 0.7739 (p-80) REVERT: I 154 MET cc_start: 0.7373 (ppp) cc_final: 0.6614 (ppp) REVERT: I 258 TYR cc_start: 0.6987 (p90) cc_final: 0.6406 (p90) REVERT: I 263 LEU cc_start: 0.9150 (tt) cc_final: 0.8631 (mp) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1466 time to fit residues: 57.6926 Evaluate side-chains 190 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 103 optimal weight: 0.0040 chunk 116 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN I 17 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.081628 restraints weight = 48973.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083808 restraints weight = 29790.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085317 restraints weight = 20898.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086336 restraints weight = 16201.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087057 restraints weight = 13521.570| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17807 Z= 0.121 Angle : 0.684 14.050 24273 Z= 0.346 Chirality : 0.045 0.317 2760 Planarity : 0.006 0.092 3184 Dihedral : 6.854 57.483 2401 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.50 % Favored : 90.45 % Rotamer: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.17), residues: 2178 helix: -0.56 (0.20), residues: 681 sheet: -1.90 (0.27), residues: 330 loop : -2.86 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG F 67 TYR 0.010 0.001 TYR H 258 PHE 0.021 0.001 PHE H 426 TRP 0.034 0.002 TRP G 42 HIS 0.006 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00275 (17807) covalent geometry : angle 0.68390 (24273) hydrogen bonds : bond 0.04107 ( 486) hydrogen bonds : angle 5.18070 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5507 (mmt) cc_final: 0.5192 (mmt) REVERT: D 237 PHE cc_start: 0.7754 (p90) cc_final: 0.7518 (t80) REVERT: D 238 TRP cc_start: 0.6906 (m100) cc_final: 0.5898 (m100) REVERT: D 251 LYS cc_start: 0.8841 (tttt) cc_final: 0.8518 (ttpt) REVERT: E 292 HIS cc_start: 0.5162 (t-90) cc_final: 0.3012 (t-90) REVERT: E 296 GLU cc_start: 0.8794 (mp0) cc_final: 0.8139 (tt0) REVERT: F 36 MET cc_start: 0.8932 (mmm) cc_final: 0.8548 (mtp) REVERT: F 42 TRP cc_start: 0.5408 (m100) cc_final: 0.4220 (m-10) REVERT: F 184 PHE cc_start: 0.8500 (t80) cc_final: 0.8120 (t80) REVERT: F 310 LEU cc_start: 0.9419 (mt) cc_final: 0.9091 (mp) REVERT: G 120 GLU cc_start: 0.7571 (pm20) cc_final: 0.7252 (pp20) REVERT: G 154 MET cc_start: 0.7584 (ttp) cc_final: 0.7295 (ttp) REVERT: G 329 MET cc_start: 0.3887 (pmm) cc_final: 0.3681 (pmm) REVERT: G 397 ILE cc_start: 0.6040 (mt) cc_final: 0.5642 (mt) REVERT: G 443 LEU cc_start: 0.8128 (mt) cc_final: 0.7897 (mm) REVERT: H 15 MET cc_start: 0.8008 (mtp) cc_final: 0.7609 (mtp) REVERT: H 204 LEU cc_start: 0.8868 (tp) cc_final: 0.8504 (tt) REVERT: H 419 LEU cc_start: 0.8763 (mt) cc_final: 0.8294 (pp) REVERT: I 42 TRP cc_start: 0.6873 (m-10) cc_final: 0.6533 (m-10) REVERT: I 138 HIS cc_start: 0.8092 (p-80) cc_final: 0.7690 (p-80) REVERT: I 258 TYR cc_start: 0.7238 (p90) cc_final: 0.6644 (p90) REVERT: I 263 LEU cc_start: 0.9126 (tt) cc_final: 0.8579 (mp) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1424 time to fit residues: 54.9209 Evaluate side-chains 185 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 ASN I 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.080194 restraints weight = 49557.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082258 restraints weight = 30647.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083683 restraints weight = 21772.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084625 restraints weight = 17027.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085315 restraints weight = 14349.913| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17807 Z= 0.160 Angle : 0.702 11.734 24273 Z= 0.355 Chirality : 0.046 0.307 2760 Planarity : 0.006 0.073 3184 Dihedral : 6.774 57.372 2401 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.11 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.17), residues: 2178 helix: -0.08 (0.21), residues: 674 sheet: -1.81 (0.27), residues: 355 loop : -2.76 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 169 TYR 0.010 0.002 TYR G 427 PHE 0.021 0.002 PHE G 237 TRP 0.047 0.002 TRP G 42 HIS 0.008 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00372 (17807) covalent geometry : angle 0.70242 (24273) hydrogen bonds : bond 0.04096 ( 486) hydrogen bonds : angle 5.10516 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5658 (mmt) cc_final: 0.5311 (mmt) REVERT: D 238 TRP cc_start: 0.6978 (m100) cc_final: 0.5982 (m100) REVERT: D 251 LYS cc_start: 0.8932 (tttt) cc_final: 0.8621 (ttpt) REVERT: E 75 ASP cc_start: 0.8699 (t0) cc_final: 0.8468 (t0) REVERT: E 172 ARG cc_start: 0.6028 (ttp80) cc_final: 0.5792 (ttp80) REVERT: E 292 HIS cc_start: 0.5157 (t-90) cc_final: 0.4487 (t-90) REVERT: E 296 GLU cc_start: 0.8789 (mp0) cc_final: 0.8137 (tt0) REVERT: F 36 MET cc_start: 0.8959 (mmm) cc_final: 0.8647 (mtp) REVERT: F 184 PHE cc_start: 0.8524 (t80) cc_final: 0.8216 (t80) REVERT: G 26 ASP cc_start: 0.6902 (m-30) cc_final: 0.6201 (m-30) REVERT: G 120 GLU cc_start: 0.7585 (pm20) cc_final: 0.7266 (pp20) REVERT: G 154 MET cc_start: 0.7625 (ttp) cc_final: 0.7308 (ttp) REVERT: G 329 MET cc_start: 0.4030 (pmm) cc_final: 0.3773 (pmm) REVERT: G 397 ILE cc_start: 0.6158 (mt) cc_final: 0.5743 (mt) REVERT: G 434 ASP cc_start: 0.6548 (t70) cc_final: 0.6344 (t0) REVERT: G 436 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6170 (mtpt) REVERT: G 443 LEU cc_start: 0.8150 (mt) cc_final: 0.7939 (mm) REVERT: H 15 MET cc_start: 0.7951 (mtp) cc_final: 0.7717 (mtp) REVERT: H 26 ASP cc_start: 0.7763 (t0) cc_final: 0.7065 (t0) REVERT: H 204 LEU cc_start: 0.8894 (tp) cc_final: 0.8547 (tt) REVERT: H 356 HIS cc_start: 0.5227 (t-90) cc_final: 0.4900 (t-90) REVERT: H 436 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6827 (mmmt) REVERT: I 42 TRP cc_start: 0.6944 (m-10) cc_final: 0.6619 (m-10) REVERT: I 138 HIS cc_start: 0.8175 (p-80) cc_final: 0.7824 (p-80) REVERT: I 258 TYR cc_start: 0.7269 (p90) cc_final: 0.6682 (p90) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1480 time to fit residues: 52.6420 Evaluate side-chains 185 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 200 optimal weight: 0.0270 chunk 150 optimal weight: 5.9990 chunk 182 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 180 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.102757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083087 restraints weight = 47984.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085254 restraints weight = 29443.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086739 restraints weight = 20789.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087765 restraints weight = 16194.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088493 restraints weight = 13536.802| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17807 Z= 0.110 Angle : 0.647 12.186 24273 Z= 0.326 Chirality : 0.044 0.266 2760 Planarity : 0.005 0.074 3184 Dihedral : 6.313 54.307 2401 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.17), residues: 2178 helix: 0.26 (0.21), residues: 672 sheet: -1.63 (0.28), residues: 325 loop : -2.63 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG F 67 TYR 0.009 0.001 TYR G 265 PHE 0.012 0.001 PHE D 278 TRP 0.061 0.002 TRP G 42 HIS 0.006 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00245 (17807) covalent geometry : angle 0.64722 (24273) hydrogen bonds : bond 0.03508 ( 486) hydrogen bonds : angle 4.72784 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5651 (mmt) cc_final: 0.5409 (mmt) REVERT: D 238 TRP cc_start: 0.6862 (m100) cc_final: 0.5987 (m100) REVERT: D 251 LYS cc_start: 0.8943 (tttt) cc_final: 0.8676 (tttt) REVERT: E 198 MET cc_start: 0.8142 (mmm) cc_final: 0.7458 (mtm) REVERT: E 292 HIS cc_start: 0.4882 (t-90) cc_final: 0.4217 (t-90) REVERT: F 36 MET cc_start: 0.8885 (mmm) cc_final: 0.8672 (mtp) REVERT: F 184 PHE cc_start: 0.8501 (t80) cc_final: 0.8002 (t80) REVERT: F 196 SER cc_start: 0.8112 (m) cc_final: 0.7783 (t) REVERT: G 99 ILE cc_start: 0.9109 (mm) cc_final: 0.8830 (mm) REVERT: G 120 GLU cc_start: 0.7589 (pm20) cc_final: 0.7329 (pp20) REVERT: G 154 MET cc_start: 0.7381 (ttp) cc_final: 0.7165 (ttp) REVERT: G 397 ILE cc_start: 0.6152 (mt) cc_final: 0.5693 (mt) REVERT: G 436 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6228 (mtpt) REVERT: H 189 LEU cc_start: 0.9201 (mt) cc_final: 0.8970 (mp) REVERT: H 204 LEU cc_start: 0.8861 (tp) cc_final: 0.8567 (tt) REVERT: H 329 MET cc_start: 0.6968 (mmp) cc_final: 0.6513 (mmp) REVERT: H 356 HIS cc_start: 0.5345 (t-90) cc_final: 0.4865 (t-90) REVERT: H 436 LYS cc_start: 0.7059 (mmpt) cc_final: 0.6854 (mmmt) REVERT: I 1 MET cc_start: 0.7704 (ttm) cc_final: 0.7376 (ttm) REVERT: I 42 TRP cc_start: 0.6756 (m-10) cc_final: 0.6432 (m-10) REVERT: I 138 HIS cc_start: 0.8054 (p-80) cc_final: 0.7744 (p-80) REVERT: I 154 MET cc_start: 0.7146 (ptm) cc_final: 0.6605 (ppp) REVERT: I 258 TYR cc_start: 0.7183 (p90) cc_final: 0.6597 (p90) REVERT: I 263 LEU cc_start: 0.9066 (tt) cc_final: 0.8858 (mp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1477 time to fit residues: 57.5909 Evaluate side-chains 204 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 167 optimal weight: 5.9990 chunk 45 optimal weight: 0.0170 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 213 optimal weight: 0.8980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081929 restraints weight = 48836.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084043 restraints weight = 30270.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085500 restraints weight = 21485.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086401 restraints weight = 16784.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087163 restraints weight = 14194.235| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17807 Z= 0.123 Angle : 0.655 11.298 24273 Z= 0.327 Chirality : 0.044 0.271 2760 Planarity : 0.005 0.066 3184 Dihedral : 6.178 52.797 2401 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.06 % Favored : 89.90 % Rotamer: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.18), residues: 2178 helix: 0.42 (0.21), residues: 668 sheet: -1.56 (0.29), residues: 305 loop : -2.57 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 121 TYR 0.009 0.001 TYR G 265 PHE 0.020 0.001 PHE G 237 TRP 0.048 0.002 TRP I 238 HIS 0.007 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00283 (17807) covalent geometry : angle 0.65517 (24273) hydrogen bonds : bond 0.03459 ( 486) hydrogen bonds : angle 4.69322 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 TRP cc_start: 0.6913 (m100) cc_final: 0.5985 (m100) REVERT: D 251 LYS cc_start: 0.9002 (tttt) cc_final: 0.8696 (ttpt) REVERT: E 198 MET cc_start: 0.8192 (mmm) cc_final: 0.7496 (mtm) REVERT: E 292 HIS cc_start: 0.5039 (t-90) cc_final: 0.4032 (t-90) REVERT: F 4 TYR cc_start: 0.8720 (m-80) cc_final: 0.8462 (m-80) REVERT: F 162 TRP cc_start: 0.7216 (t-100) cc_final: 0.6830 (t-100) REVERT: F 184 PHE cc_start: 0.8516 (t80) cc_final: 0.8086 (t80) REVERT: F 196 SER cc_start: 0.8096 (m) cc_final: 0.7768 (t) REVERT: G 120 GLU cc_start: 0.7574 (pm20) cc_final: 0.7323 (pp20) REVERT: G 397 ILE cc_start: 0.6216 (mt) cc_final: 0.5739 (mt) REVERT: G 434 ASP cc_start: 0.5851 (t0) cc_final: 0.4678 (p0) REVERT: H 204 LEU cc_start: 0.8877 (tp) cc_final: 0.8602 (tt) REVERT: H 356 HIS cc_start: 0.5393 (t-90) cc_final: 0.4753 (t-90) REVERT: H 436 LYS cc_start: 0.7094 (mmpt) cc_final: 0.6880 (mmmt) REVERT: I 42 TRP cc_start: 0.6838 (m-10) cc_final: 0.6495 (m-10) REVERT: I 138 HIS cc_start: 0.8087 (p-80) cc_final: 0.7803 (p-80) REVERT: I 154 MET cc_start: 0.7155 (ptm) cc_final: 0.6684 (ppp) REVERT: I 258 TYR cc_start: 0.7157 (p90) cc_final: 0.6541 (p90) REVERT: I 263 LEU cc_start: 0.9073 (tt) cc_final: 0.8852 (mp) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.1502 time to fit residues: 54.3301 Evaluate side-chains 197 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 209 optimal weight: 0.0570 chunk 73 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** G 140 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 = 0.3505 r_free = 0.3505 target = 0.099328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079814 restraints weight = 49176.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081910 restraints weight = 30473.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083331 restraints weight = 21630.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084312 restraints weight = 16929.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085001 restraints weight = 14216.693| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17807 Z= 0.167 Angle : 0.713 10.945 24273 Z= 0.357 Chirality : 0.046 0.279 2760 Planarity : 0.006 0.100 3184 Dihedral : 6.355 56.558 2401 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.18), residues: 2178 helix: 0.48 (0.21), residues: 661 sheet: -1.56 (0.28), residues: 337 loop : -2.54 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 123 TYR 0.012 0.002 TYR G 265 PHE 0.031 0.002 PHE H 362 TRP 0.067 0.003 TRP G 42 HIS 0.013 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00393 (17807) covalent geometry : angle 0.71340 (24273) hydrogen bonds : bond 0.03871 ( 486) hydrogen bonds : angle 4.85124 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.7942 (mtt) cc_final: 0.7676 (mtt) REVERT: D 129 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7443 (mtm180) REVERT: D 154 MET cc_start: 0.7546 (ttm) cc_final: 0.7336 (ttm) REVERT: D 238 TRP cc_start: 0.6975 (m100) cc_final: 0.5979 (m100) REVERT: D 251 LYS cc_start: 0.9014 (tttt) cc_final: 0.8719 (ttpt) REVERT: E 5 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7855 (ttp-170) REVERT: E 267 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8381 (mm-30) REVERT: E 292 HIS cc_start: 0.5084 (t-90) cc_final: 0.4225 (t-90) REVERT: E 296 GLU cc_start: 0.8813 (mp0) cc_final: 0.8005 (tt0) REVERT: F 196 SER cc_start: 0.8088 (m) cc_final: 0.7780 (t) REVERT: G 120 GLU cc_start: 0.7541 (pm20) cc_final: 0.7327 (pp20) REVERT: G 329 MET cc_start: 0.3450 (pmm) cc_final: 0.3218 (pmm) REVERT: G 397 ILE cc_start: 0.6121 (mt) cc_final: 0.5669 (mt) REVERT: H 204 LEU cc_start: 0.8874 (tp) cc_final: 0.8665 (tt) REVERT: H 329 MET cc_start: 0.6979 (mmp) cc_final: 0.6755 (mmp) REVERT: H 346 TRP cc_start: 0.7671 (m100) cc_final: 0.7380 (m100) REVERT: H 356 HIS cc_start: 0.5753 (t-90) cc_final: 0.5123 (t-90) REVERT: H 436 LYS cc_start: 0.7129 (mmpt) cc_final: 0.6896 (mmmt) REVERT: I 42 TRP cc_start: 0.6995 (m-10) cc_final: 0.6628 (m-10) REVERT: I 138 HIS cc_start: 0.8046 (p-80) cc_final: 0.7822 (p-80) REVERT: I 258 TYR cc_start: 0.7164 (p90) cc_final: 0.6642 (p90) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1462 time to fit residues: 51.3050 Evaluate side-chains 194 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 142 optimal weight: 5.9990 chunk 203 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN I 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082622 restraints weight = 48209.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084804 restraints weight = 29501.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086312 restraints weight = 20782.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087348 restraints weight = 16154.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088069 restraints weight = 13483.837| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17807 Z= 0.106 Angle : 0.638 12.677 24273 Z= 0.320 Chirality : 0.043 0.274 2760 Planarity : 0.005 0.081 3184 Dihedral : 5.983 52.832 2401 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.63 % Favored : 91.32 % Rotamer: Outliers : 0.05 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.18), residues: 2178 helix: 0.84 (0.21), residues: 655 sheet: -1.43 (0.29), residues: 315 loop : -2.46 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.011 0.001 TYR G 265 PHE 0.027 0.001 PHE G 237 TRP 0.055 0.002 TRP G 42 HIS 0.005 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00238 (17807) covalent geometry : angle 0.63810 (24273) hydrogen bonds : bond 0.03257 ( 486) hydrogen bonds : angle 4.51669 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7402 (mtm180) REVERT: D 154 MET cc_start: 0.7405 (ttm) cc_final: 0.7126 (ttm) REVERT: D 238 TRP cc_start: 0.6981 (m100) cc_final: 0.6074 (m100) REVERT: D 251 LYS cc_start: 0.8977 (tttt) cc_final: 0.8686 (tttt) REVERT: E 198 MET cc_start: 0.8280 (mmm) cc_final: 0.7432 (mtm) REVERT: E 292 HIS cc_start: 0.5568 (t-90) cc_final: 0.4126 (t-90) REVERT: F 82 LEU cc_start: 0.6804 (tp) cc_final: 0.6530 (tp) REVERT: F 184 PHE cc_start: 0.8505 (t80) cc_final: 0.7997 (t80) REVERT: G 15 MET cc_start: 0.7612 (mtt) cc_final: 0.7225 (mtt) REVERT: G 120 GLU cc_start: 0.7591 (pm20) cc_final: 0.7346 (pp20) REVERT: G 154 MET cc_start: 0.7896 (ttm) cc_final: 0.7567 (tmm) REVERT: G 397 ILE cc_start: 0.6379 (mt) cc_final: 0.5844 (mt) REVERT: G 434 ASP cc_start: 0.5881 (t0) cc_final: 0.5435 (t0) REVERT: H 329 MET cc_start: 0.7130 (mmp) cc_final: 0.6364 (mmt) REVERT: H 346 TRP cc_start: 0.7770 (m100) cc_final: 0.7506 (m100) REVERT: H 443 LEU cc_start: 0.6846 (pp) cc_final: 0.6475 (mp) REVERT: I 154 MET cc_start: 0.6957 (ptm) cc_final: 0.6426 (ppp) REVERT: I 258 TYR cc_start: 0.7101 (p90) cc_final: 0.6505 (p90) outliers start: 1 outliers final: 1 residues processed: 247 average time/residue: 0.1547 time to fit residues: 56.3347 Evaluate side-chains 187 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 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 = 0.3539 r_free = 0.3539 target = 0.101486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081961 restraints weight = 48800.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084078 restraints weight = 30229.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085553 restraints weight = 21448.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086552 restraints weight = 16736.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087164 restraints weight = 14031.749| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17807 Z= 0.123 Angle : 0.652 11.806 24273 Z= 0.326 Chirality : 0.044 0.276 2760 Planarity : 0.005 0.079 3184 Dihedral : 5.933 51.951 2401 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.83 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.18), residues: 2178 helix: 0.92 (0.21), residues: 657 sheet: -1.35 (0.29), residues: 315 loop : -2.43 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 123 TYR 0.011 0.001 TYR G 265 PHE 0.027 0.001 PHE H 426 TRP 0.054 0.002 TRP G 42 HIS 0.007 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00289 (17807) covalent geometry : angle 0.65176 (24273) hydrogen bonds : bond 0.03380 ( 486) hydrogen bonds : angle 4.50624 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7423 (mtm180) REVERT: D 238 TRP cc_start: 0.6465 (m100) cc_final: 0.6024 (m100) REVERT: D 251 LYS cc_start: 0.8993 (tttt) cc_final: 0.8700 (tttt) REVERT: E 198 MET cc_start: 0.8328 (mmm) cc_final: 0.7472 (mtm) REVERT: E 292 HIS cc_start: 0.5165 (t-90) cc_final: 0.4242 (t-90) REVERT: F 82 LEU cc_start: 0.6735 (tp) cc_final: 0.6488 (tp) REVERT: F 184 PHE cc_start: 0.8531 (t80) cc_final: 0.8037 (t80) REVERT: G 99 ILE cc_start: 0.9066 (mm) cc_final: 0.8815 (mm) REVERT: G 397 ILE cc_start: 0.6348 (mt) cc_final: 0.5627 (mt) REVERT: G 434 ASP cc_start: 0.5726 (t0) cc_final: 0.5307 (t0) REVERT: H 346 TRP cc_start: 0.7768 (m100) cc_final: 0.7496 (m100) REVERT: H 353 MET cc_start: 0.5818 (ppp) cc_final: 0.5479 (tmm) REVERT: H 436 LYS cc_start: 0.7007 (mmpt) cc_final: 0.6756 (mmmt) REVERT: I 258 TYR cc_start: 0.7036 (p90) cc_final: 0.6425 (p90) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1437 time to fit residues: 48.4722 Evaluate side-chains 181 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 111 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 76 optimal weight: 0.0270 chunk 202 optimal weight: 0.9990 chunk 107 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 87 optimal weight: 0.1980 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084489 restraints weight = 47870.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086551 restraints weight = 30352.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087973 restraints weight = 21891.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088893 restraints weight = 17301.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089604 restraints weight = 14755.947| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17807 Z= 0.108 Angle : 0.641 11.227 24273 Z= 0.320 Chirality : 0.043 0.271 2760 Planarity : 0.005 0.078 3184 Dihedral : 5.700 48.511 2401 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.18), residues: 2178 helix: 1.04 (0.21), residues: 663 sheet: -1.32 (0.30), residues: 306 loop : -2.37 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 219 TYR 0.010 0.001 TYR G 265 PHE 0.020 0.001 PHE D 229 TRP 0.048 0.002 TRP G 42 HIS 0.005 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00245 (17807) covalent geometry : angle 0.64135 (24273) hydrogen bonds : bond 0.03057 ( 486) hydrogen bonds : angle 4.32157 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 251 LYS cc_start: 0.8767 (tttt) cc_final: 0.8508 (ttpt) REVERT: E 292 HIS cc_start: 0.5465 (t-90) cc_final: 0.4074 (t-90) REVERT: F 76 THR cc_start: 0.8359 (p) cc_final: 0.8130 (p) REVERT: F 82 LEU cc_start: 0.6636 (tp) cc_final: 0.6392 (tp) REVERT: F 184 PHE cc_start: 0.8500 (t80) cc_final: 0.7959 (t80) REVERT: G 26 ASP cc_start: 0.6606 (m-30) cc_final: 0.5493 (m-30) REVERT: G 99 ILE cc_start: 0.8991 (mm) cc_final: 0.8685 (mm) REVERT: G 154 MET cc_start: 0.7497 (ttm) cc_final: 0.7278 (tmm) REVERT: G 190 THR cc_start: 0.8278 (p) cc_final: 0.7723 (t) REVERT: G 434 ASP cc_start: 0.6028 (t0) cc_final: 0.5641 (t0) REVERT: H 329 MET cc_start: 0.7144 (mmp) cc_final: 0.6932 (mmp) REVERT: H 346 TRP cc_start: 0.7781 (m100) cc_final: 0.7525 (m100) REVERT: H 353 MET cc_start: 0.5591 (ppp) cc_final: 0.5231 (tmm) REVERT: H 436 LYS cc_start: 0.7039 (mmpt) cc_final: 0.6769 (mmmt) REVERT: I 203 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7587 (tm-30) REVERT: I 258 TYR cc_start: 0.6988 (p90) cc_final: 0.6395 (p90) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1386 time to fit residues: 50.8217 Evaluate side-chains 192 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 46 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 154 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082093 restraints weight = 48740.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084074 restraints weight = 30919.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085429 restraints weight = 22365.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086361 restraints weight = 17798.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087044 restraints weight = 15136.550| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17807 Z= 0.135 Angle : 0.675 12.166 24273 Z= 0.334 Chirality : 0.044 0.276 2760 Planarity : 0.005 0.077 3184 Dihedral : 5.817 53.196 2401 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.05 % Allowed : 0.21 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.18), residues: 2178 helix: 1.08 (0.21), residues: 663 sheet: -1.22 (0.29), residues: 323 loop : -2.39 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 219 TYR 0.013 0.001 TYR G 265 PHE 0.025 0.001 PHE I 229 TRP 0.067 0.002 TRP G 42 HIS 0.008 0.001 HIS H 292 Details of bonding type rmsd covalent geometry : bond 0.00319 (17807) covalent geometry : angle 0.67547 (24273) hydrogen bonds : bond 0.03359 ( 486) hydrogen bonds : angle 4.44421 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.34 seconds wall clock time: 48 minutes 13.13 seconds (2893.13 seconds total)