Starting phenix.real_space_refine on Fri Sep 11 21:07:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wc0_8794/09_2026/5wc0_8794.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 42 5.16 5 C 7182 2.51 5 N 1990 2.21 5 O 2228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1865 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 168 Chain: "B" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1888 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1875 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 168 Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 161 Chain: "E" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 161 Chain: "F" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 6, 'TRP:plan': 2, 'GLU:plan': 10, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.98, per 1000 atoms: 0.26 Number of scatterers: 11460 At special positions: 0 Unit cell: (129.69, 138.86, 103.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 18 15.00 O 2228 8.00 N 1990 7.00 C 7182 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 682.7 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 12 sheets defined 54.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 198 through 209 removed outlier: 3.596A pdb=" N LYS A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.179A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 4.282A pdb=" N VAL A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 4.013A pdb=" N LEU A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.821A pdb=" N ARG A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 415 removed outlier: 3.589A pdb=" N VAL A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.696A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.583A pdb=" N GLU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.777A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.251A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.604A pdb=" N GLU B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 4.097A pdb=" N LEU B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.641A pdb=" N GLU B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.726A pdb=" N LEU B 389 " --> pdb=" O ASN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 416 removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 440 through 449 removed outlier: 4.069A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.984A pdb=" N ARG C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 Processing helix chain 'C' and resid 209 through 215 removed outlier: 4.219A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.655A pdb=" N ALA C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.767A pdb=" N GLU C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.581A pdb=" N LEU C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 363 through 375 removed outlier: 3.780A pdb=" N ARG C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 392 removed outlier: 3.800A pdb=" N ARG C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 415 removed outlier: 4.264A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 450 removed outlier: 4.133A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 removed outlier: 4.375A pdb=" N MET C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.035A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 238 through 250 removed outlier: 4.509A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 284 Processing helix chain 'D' and resid 308 through 322 removed outlier: 4.200A pdb=" N LEU D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.860A pdb=" N ARG D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 375 Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.936A pdb=" N ARG D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.197A pdb=" N LEU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 439 through 450 removed outlier: 3.675A pdb=" N PHE D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 removed outlier: 4.083A pdb=" N ASP D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.549A pdb=" N LYS E 202 " --> pdb=" O MET E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.734A pdb=" N LEU E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 239 through 250 removed outlier: 4.320A pdb=" N ALA E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA E 245 " --> pdb=" O LEU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 285 Processing helix chain 'E' and resid 308 through 321 removed outlier: 4.610A pdb=" N LEU E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.814A pdb=" N ARG E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'E' and resid 385 through 393 removed outlier: 4.078A pdb=" N ARG E 392 " --> pdb=" O ASP E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 416 removed outlier: 3.658A pdb=" N VAL E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 Processing helix chain 'E' and resid 439 through 450 removed outlier: 3.940A pdb=" N ALA E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 Processing helix chain 'F' and resid 175 through 182 Processing helix chain 'F' and resid 198 through 208 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.806A pdb=" N ALA F 245 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 285 removed outlier: 3.619A pdb=" N ARG F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.758A pdb=" N LEU F 318 " --> pdb=" O LYS F 314 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL F 319 " --> pdb=" O SER F 315 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.680A pdb=" N GLU F 344 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 353 Processing helix chain 'F' and resid 363 through 375 Processing helix chain 'F' and resid 385 through 391 Processing helix chain 'F' and resid 397 through 416 removed outlier: 4.093A pdb=" N LEU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 439 through 450 removed outlier: 4.187A pdb=" N ALA F 445 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 466 removed outlier: 3.752A pdb=" N MET F 459 " --> pdb=" O GLY F 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 231 removed outlier: 7.431A pdb=" N VAL A 230 " --> pdb=" O ILE A 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 256 removed outlier: 6.536A pdb=" N THR A 253 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N PHE A 290 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 255 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.669A pdb=" N ALA B 183 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 254 " --> pdb=" O ALA B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.647A pdb=" N VAL B 230 " --> pdb=" O ILE B 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 288 through 290 removed outlier: 6.175A pdb=" N ILE B 289 " --> pdb=" O LEU B 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 232 Processing sheet with id=AA7, first strand: chain 'C' and resid 288 through 292 removed outlier: 3.647A pdb=" N ALA C 338 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.658A pdb=" N ALA D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE D 254 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER D 287 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 229 through 232 Processing sheet with id=AB1, first strand: chain 'E' and resid 182 through 183 removed outlier: 4.254A pdb=" N ALA E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE E 254 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE E 255 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AB3, first strand: chain 'F' and resid 253 through 255 removed outlier: 6.819A pdb=" N THR F 253 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N PHE F 290 " --> pdb=" O THR F 253 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE F 255 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP F 292 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER F 287 " --> pdb=" O PHE F 334 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU F 336 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE F 289 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA F 338 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 291 " --> pdb=" O ALA F 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 484 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3880 1.34 - 1.46: 2354 1.46 - 1.58: 5303 1.58 - 1.69: 30 1.69 - 1.81: 66 Bond restraints: 11633 Sorted by residual: bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 15846 4.61 - 9.22: 83 9.22 - 13.82: 3 13.82 - 18.43: 3 18.43 - 23.04: 10 Bond angle restraints: 15945 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 116.83 23.04 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 115.67 21.16 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.28e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.35 20.52 1.00e+00 1.00e+00 4.21e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 ... (remaining 15940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 6612 15.74 - 31.47: 225 31.47 - 47.21: 16 47.21 - 62.95: 4 62.95 - 78.68: 3 Dihedral angle restraints: 6860 sinusoidal: 2056 harmonic: 4804 Sorted by residual: dihedral pdb=" CA ASP E 363 " pdb=" C ASP E 363 " pdb=" N ILE E 364 " pdb=" CA ILE E 364 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA PRO D 360 " pdb=" C PRO D 360 " pdb=" N LEU D 361 " pdb=" CA LEU D 361 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ASP F 363 " pdb=" C ASP F 363 " pdb=" N ILE F 364 " pdb=" CA ILE F 364 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 6857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1792 0.077 - 0.154: 159 0.154 - 0.230: 6 0.230 - 0.307: 7 0.307 - 0.384: 2 Chirality restraints: 1966 Sorted by residual: chirality pdb=" CA LEU D 345 " pdb=" N LEU D 345 " pdb=" C LEU D 345 " pdb=" CB LEU D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ARG C 422 " pdb=" N ARG C 422 " pdb=" C ARG C 422 " pdb=" CB ARG C 422 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA LEU B 345 " pdb=" N LEU B 345 " pdb=" C LEU B 345 " pdb=" CB LEU B 345 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1963 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 343 " -0.013 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C TRP D 343 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP D 343 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 344 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 359 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO F 360 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 360 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 360 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 343 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C TRP B 343 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 343 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 344 " 0.016 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 161 2.61 - 3.19: 11456 3.19 - 3.76: 17092 3.76 - 4.33: 23818 4.33 - 4.90: 35676 Nonbonded interactions: 88203 Sorted by model distance: nonbonded pdb=" OG SER B 252 " pdb=" O PRO B 286 " model vdw 2.043 3.040 nonbonded pdb=" OG SER A 252 " pdb=" O PRO A 286 " model vdw 2.044 3.040 nonbonded pdb=" OG SER C 451 " pdb=" O ASP D 467 " model vdw 2.068 3.040 nonbonded pdb=" O ASP B 417 " pdb=" OG SER B 420 " model vdw 2.070 3.040 nonbonded pdb=" O ALA A 390 " pdb=" OG1 THR A 393 " model vdw 2.081 3.040 ... (remaining 88198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 173 through 282 or (resid 283 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'C' and (resid 173 through 470 or resid 501)) selection = (chain 'D' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'E' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'F' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ } 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: 2.700 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.290 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.010 0.888 11634 Z= 0.914 Angle : 1.062 23.038 15945 Z= 0.790 Chirality : 0.047 0.384 1966 Planarity : 0.005 0.069 2061 Dihedral : 8.992 78.683 3708 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.88 % Favored : 91.87 % Rotamer: Outliers : 0.11 % Allowed : 0.96 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.17), residues: 1612 helix: -3.33 (0.12), residues: 823 sheet: -3.02 (0.32), residues: 168 loop : -2.68 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 351 TYR 0.012 0.002 TYR E 284 PHE 0.016 0.002 PHE F 334 TRP 0.019 0.002 TRP A 465 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.40 (11633) covalent geometry : angle 1.06244 / 0.79 (15945) hydrogen bonds : bond 0.17515 / 11.82 ( 484) hydrogen bonds : angle 9.70112 / 6.81 ( 1398) Misc. bond : bond 0.88791 / 46.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8669 (tt0) cc_final: 0.8404 (tm-30) REVERT: A 372 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8837 (mm-30) REVERT: B 239 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8416 (mtmt) REVERT: B 375 MET cc_start: 0.8980 (mmm) cc_final: 0.8371 (mmm) REVERT: C 207 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 229 MET cc_start: 0.8892 (ptp) cc_final: 0.8598 (ptp) REVERT: C 239 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8253 (mtmt) REVERT: C 249 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8586 (tm-30) REVERT: C 336 LEU cc_start: 0.9202 (tp) cc_final: 0.8791 (tt) REVERT: C 371 ILE cc_start: 0.9376 (mt) cc_final: 0.8940 (mt) REVERT: C 448 GLN cc_start: 0.9400 (pt0) cc_final: 0.8862 (pt0) REVERT: D 293 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7193 (mm110) REVERT: D 372 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8063 (mt-10) REVERT: E 203 GLN cc_start: 0.8856 (tt0) cc_final: 0.8357 (tp40) REVERT: E 219 PHE cc_start: 0.9038 (m-80) cc_final: 0.8808 (m-80) REVERT: E 229 MET cc_start: 0.8308 (ptp) cc_final: 0.8108 (ptt) REVERT: E 411 ASN cc_start: 0.9120 (t0) cc_final: 0.8710 (t0) REVERT: F 206 HIS cc_start: 0.8315 (t-90) cc_final: 0.8071 (t-170) REVERT: F 385 ASN cc_start: 0.9180 (t0) cc_final: 0.8967 (t0) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1057 time to fit residues: 35.1150 Evaluate side-chains 137 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 440 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS E 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.060778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048714 restraints weight = 87885.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049779 restraints weight = 60676.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050591 restraints weight = 45536.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051223 restraints weight = 36438.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.051676 restraints weight = 30633.357| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11634 Z= 0.147 Angle : 0.600 6.750 15945 Z= 0.327 Chirality : 0.043 0.202 1966 Planarity : 0.005 0.058 2061 Dihedral : 7.869 89.977 1742 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.11 % Allowed : 1.06 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.19), residues: 1612 helix: -1.99 (0.15), residues: 824 sheet: -2.40 (0.32), residues: 185 loop : -1.79 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 392 TYR 0.014 0.001 TYR E 386 PHE 0.014 0.001 PHE F 317 TRP 0.025 0.001 TRP A 465 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (11633) covalent geometry : angle 0.59952 / 0.33 (15945) hydrogen bonds : bond 0.04657 / 3.12 ( 484) hydrogen bonds : angle 5.70093 / 3.99 ( 1398) Misc. bond : bond 0.00413 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8851 (tt0) cc_final: 0.8549 (mt0) REVERT: A 229 MET cc_start: 0.6823 (pmm) cc_final: 0.6595 (pmm) REVERT: A 372 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8870 (mm-30) REVERT: B 198 MET cc_start: 0.9032 (mpp) cc_final: 0.8797 (mpp) REVERT: B 239 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8681 (mttp) REVERT: C 207 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6846 (mt-10) REVERT: C 239 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8324 (mtmt) REVERT: C 371 ILE cc_start: 0.9360 (mt) cc_final: 0.8556 (tt) REVERT: C 400 ASP cc_start: 0.8751 (m-30) cc_final: 0.8487 (t0) REVERT: D 203 GLN cc_start: 0.9346 (tt0) cc_final: 0.8304 (tm-30) REVERT: D 207 GLU cc_start: 0.8032 (pt0) cc_final: 0.6621 (pt0) REVERT: D 293 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7073 (mm110) REVERT: D 372 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 375 MET cc_start: 0.8583 (mmm) cc_final: 0.8197 (tpt) REVERT: E 219 PHE cc_start: 0.9123 (m-80) cc_final: 0.8870 (m-80) REVERT: E 336 LEU cc_start: 0.9455 (tp) cc_final: 0.9176 (tt) REVERT: E 407 THR cc_start: 0.9616 (m) cc_final: 0.9159 (p) REVERT: E 411 ASN cc_start: 0.9128 (t0) cc_final: 0.8803 (m-40) REVERT: E 414 ARG cc_start: 0.9007 (mtp180) cc_final: 0.8805 (mtm110) REVERT: F 206 HIS cc_start: 0.8866 (t-90) cc_final: 0.8531 (t-170) REVERT: F 207 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0870 time to fit residues: 22.8619 Evaluate side-chains 135 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 0.0060 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.061148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048799 restraints weight = 87439.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049908 restraints weight = 60273.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050754 restraints weight = 45251.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051400 restraints weight = 36112.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051795 restraints weight = 30387.435| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11634 Z= 0.115 Angle : 0.536 7.180 15945 Z= 0.289 Chirality : 0.041 0.143 1966 Planarity : 0.005 0.051 2061 Dihedral : 7.220 88.722 1742 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.21 % Allowed : 1.38 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.20), residues: 1612 helix: -1.21 (0.16), residues: 823 sheet: -1.85 (0.34), residues: 185 loop : -1.29 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 311 TYR 0.008 0.001 TYR C 386 PHE 0.012 0.001 PHE D 396 TRP 0.024 0.001 TRP A 465 HIS 0.003 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11633) covalent geometry : angle 0.53567 / 0.29 (15945) hydrogen bonds : bond 0.04011 / 2.71 ( 484) hydrogen bonds : angle 4.98210 / 3.50 ( 1398) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8823 (mm-30) REVERT: A 375 MET cc_start: 0.8514 (tpt) cc_final: 0.8227 (tpp) REVERT: A 410 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 198 MET cc_start: 0.8897 (mpp) cc_final: 0.8674 (mpp) REVERT: B 239 LYS cc_start: 0.9057 (mtmm) cc_final: 0.8690 (mttp) REVERT: B 380 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7892 (ptmt) REVERT: C 239 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8444 (mtmt) REVERT: C 371 ILE cc_start: 0.9361 (mt) cc_final: 0.8983 (mm) REVERT: D 203 GLN cc_start: 0.9448 (tt0) cc_final: 0.8311 (tm-30) REVERT: D 207 GLU cc_start: 0.7983 (pt0) cc_final: 0.6155 (pt0) REVERT: D 293 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7104 (mm110) REVERT: D 372 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7959 (mt-10) REVERT: D 375 MET cc_start: 0.8689 (mmm) cc_final: 0.7581 (tpt) REVERT: E 219 PHE cc_start: 0.9108 (m-80) cc_final: 0.8839 (m-80) REVERT: E 336 LEU cc_start: 0.9358 (tp) cc_final: 0.9000 (tt) REVERT: E 375 MET cc_start: 0.9004 (tpp) cc_final: 0.8772 (tpp) REVERT: E 407 THR cc_start: 0.9614 (m) cc_final: 0.9175 (p) REVERT: E 411 ASN cc_start: 0.9136 (t0) cc_final: 0.8800 (m-40) REVERT: E 414 ARG cc_start: 0.9012 (mtp180) cc_final: 0.8785 (mtm110) REVERT: F 206 HIS cc_start: 0.8840 (t-90) cc_final: 0.8553 (t-170) REVERT: F 207 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8064 (mt-10) REVERT: F 229 MET cc_start: 0.8692 (pmm) cc_final: 0.8407 (pmm) REVERT: F 375 MET cc_start: 0.8539 (mmp) cc_final: 0.8250 (mmm) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.0876 time to fit residues: 24.2038 Evaluate side-chains 131 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 92 optimal weight: 0.0570 chunk 153 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.060214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048066 restraints weight = 87249.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049195 restraints weight = 59631.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050027 restraints weight = 44457.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050675 restraints weight = 35381.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051146 restraints weight = 29546.143| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11634 Z= 0.105 Angle : 0.509 7.514 15945 Z= 0.270 Chirality : 0.040 0.135 1966 Planarity : 0.004 0.048 2061 Dihedral : 6.667 87.888 1742 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.11 % Allowed : 0.96 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1612 helix: -0.50 (0.18), residues: 827 sheet: -1.10 (0.37), residues: 180 loop : -0.80 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 367 TYR 0.043 0.001 TYR F 284 PHE 0.010 0.001 PHE E 218 TRP 0.007 0.001 TRP D 465 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (11633) covalent geometry : angle 0.50934 / 0.27 (15945) hydrogen bonds : bond 0.03462 / 2.35 ( 484) hydrogen bonds : angle 4.38758 / 3.07 ( 1398) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8783 (mm-30) REVERT: B 198 MET cc_start: 0.8830 (mpp) cc_final: 0.8614 (mpp) REVERT: B 380 LYS cc_start: 0.8397 (ptmt) cc_final: 0.8093 (ptmt) REVERT: C 198 MET cc_start: 0.8666 (mtm) cc_final: 0.8285 (mtm) REVERT: C 239 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8579 (mtmt) REVERT: C 254 PHE cc_start: 0.8269 (t80) cc_final: 0.7871 (t80) REVERT: C 371 ILE cc_start: 0.9366 (mt) cc_final: 0.9088 (mm) REVERT: D 203 GLN cc_start: 0.9404 (tt0) cc_final: 0.8260 (tm-30) REVERT: D 207 GLU cc_start: 0.7949 (pt0) cc_final: 0.6283 (pt0) REVERT: D 293 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7319 (mm110) REVERT: D 372 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 375 MET cc_start: 0.8833 (mmm) cc_final: 0.7955 (tpt) REVERT: E 193 ASP cc_start: 0.8997 (m-30) cc_final: 0.8411 (t0) REVERT: E 203 GLN cc_start: 0.8752 (tt0) cc_final: 0.8294 (tp-100) REVERT: E 219 PHE cc_start: 0.9087 (m-80) cc_final: 0.8777 (m-80) REVERT: E 336 LEU cc_start: 0.9349 (tp) cc_final: 0.8993 (tt) REVERT: E 372 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8369 (tp30) REVERT: F 206 HIS cc_start: 0.8922 (t-90) cc_final: 0.8670 (t-170) REVERT: F 229 MET cc_start: 0.8686 (pmm) cc_final: 0.8317 (pmm) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.0834 time to fit residues: 23.3480 Evaluate side-chains 130 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 GLN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN F 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047718 restraints weight = 88290.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048827 restraints weight = 60191.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049609 restraints weight = 44886.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050275 restraints weight = 35829.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050686 restraints weight = 30006.895| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11634 Z= 0.115 Angle : 0.505 9.057 15945 Z= 0.267 Chirality : 0.040 0.132 1966 Planarity : 0.004 0.050 2061 Dihedral : 6.477 87.911 1742 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.11 % Allowed : 1.17 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1612 helix: -0.18 (0.18), residues: 852 sheet: -0.72 (0.38), residues: 185 loop : -0.82 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 439 TYR 0.008 0.001 TYR F 416 PHE 0.011 0.001 PHE D 278 TRP 0.009 0.001 TRP E 465 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11633) covalent geometry : angle 0.50515 / 0.27 (15945) hydrogen bonds : bond 0.03172 / 2.14 ( 484) hydrogen bonds : angle 4.23728 / 2.97 ( 1398) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6199 (pmm) cc_final: 0.5757 (ppp) REVERT: A 372 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8684 (mm-30) REVERT: A 394 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 198 MET cc_start: 0.8795 (mpp) cc_final: 0.8562 (mpp) REVERT: B 380 LYS cc_start: 0.8425 (ptmt) cc_final: 0.8125 (ptmt) REVERT: C 198 MET cc_start: 0.8728 (mtm) cc_final: 0.8521 (mtm) REVERT: C 254 PHE cc_start: 0.8310 (t80) cc_final: 0.7867 (t80) REVERT: C 371 ILE cc_start: 0.9399 (mt) cc_final: 0.8814 (tp) REVERT: D 203 GLN cc_start: 0.9415 (tt0) cc_final: 0.8306 (tm-30) REVERT: D 207 GLU cc_start: 0.8067 (pt0) cc_final: 0.6277 (pt0) REVERT: D 293 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7242 (mp10) REVERT: D 372 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7508 (mp0) REVERT: D 375 MET cc_start: 0.9053 (mmm) cc_final: 0.8111 (tpt) REVERT: D 383 GLU cc_start: 0.9356 (pt0) cc_final: 0.9077 (pm20) REVERT: E 203 GLN cc_start: 0.8714 (tt0) cc_final: 0.8439 (tp-100) REVERT: E 219 PHE cc_start: 0.9132 (m-80) cc_final: 0.8866 (m-80) REVERT: E 336 LEU cc_start: 0.9262 (tp) cc_final: 0.9054 (tp) REVERT: E 372 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8367 (tp30) REVERT: E 375 MET cc_start: 0.8811 (tpp) cc_final: 0.8443 (tpp) REVERT: F 229 MET cc_start: 0.8692 (pmm) cc_final: 0.8333 (pmm) REVERT: F 430 MET cc_start: 0.4112 (mmt) cc_final: 0.3810 (mmt) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.0939 time to fit residues: 23.1607 Evaluate side-chains 126 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.058728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047135 restraints weight = 86949.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048220 restraints weight = 59212.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048972 restraints weight = 44226.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049642 restraints weight = 35241.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050074 restraints weight = 29474.704| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11634 Z= 0.117 Angle : 0.512 10.766 15945 Z= 0.269 Chirality : 0.040 0.132 1966 Planarity : 0.004 0.047 2061 Dihedral : 6.429 88.356 1742 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1612 helix: -0.00 (0.18), residues: 853 sheet: -0.56 (0.38), residues: 189 loop : -0.57 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 223 TYR 0.006 0.001 TYR A 386 PHE 0.013 0.001 PHE E 443 TRP 0.008 0.001 TRP C 465 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11633) covalent geometry : angle 0.51242 / 0.27 (15945) hydrogen bonds : bond 0.03125 / 2.10 ( 484) hydrogen bonds : angle 4.17079 / 2.92 ( 1398) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6411 (pmm) cc_final: 0.6022 (ppp) REVERT: A 394 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7068 (mp0) REVERT: B 198 MET cc_start: 0.8859 (mpp) cc_final: 0.8572 (mpp) REVERT: B 380 LYS cc_start: 0.8448 (ptmt) cc_final: 0.8101 (ptmt) REVERT: B 411 ASN cc_start: 0.9139 (m-40) cc_final: 0.8938 (m-40) REVERT: C 198 MET cc_start: 0.8691 (mtm) cc_final: 0.8462 (mtm) REVERT: C 207 GLU cc_start: 0.8232 (pt0) cc_final: 0.7488 (pp20) REVERT: C 254 PHE cc_start: 0.8368 (t80) cc_final: 0.7902 (t80) REVERT: C 371 ILE cc_start: 0.9400 (mt) cc_final: 0.8822 (tp) REVERT: D 203 GLN cc_start: 0.9387 (tt0) cc_final: 0.8637 (tm-30) REVERT: D 293 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7374 (mm110) REVERT: D 372 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7649 (mp0) REVERT: D 375 MET cc_start: 0.9042 (mmm) cc_final: 0.8043 (tpt) REVERT: D 383 GLU cc_start: 0.9373 (pt0) cc_final: 0.9136 (pm20) REVERT: E 203 GLN cc_start: 0.8722 (tt0) cc_final: 0.8412 (tp-100) REVERT: E 207 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7015 (pt0) REVERT: E 219 PHE cc_start: 0.9149 (m-80) cc_final: 0.8781 (m-80) REVERT: E 336 LEU cc_start: 0.9323 (tp) cc_final: 0.9056 (tt) REVERT: E 372 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8304 (tp30) REVERT: E 375 MET cc_start: 0.8889 (tpp) cc_final: 0.8400 (tpp) REVERT: F 207 GLU cc_start: 0.8806 (pt0) cc_final: 0.8595 (pt0) REVERT: F 229 MET cc_start: 0.8692 (pmm) cc_final: 0.8336 (pmm) REVERT: F 363 ASP cc_start: 0.9350 (m-30) cc_final: 0.8665 (p0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0951 time to fit residues: 22.8050 Evaluate side-chains 126 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 29 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 121 optimal weight: 0.0040 chunk 23 optimal weight: 0.0670 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046639 restraints weight = 86814.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047843 restraints weight = 58509.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048743 restraints weight = 43085.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049313 restraints weight = 33961.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049829 restraints weight = 28450.700| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11634 Z= 0.101 Angle : 0.515 11.091 15945 Z= 0.269 Chirality : 0.040 0.132 1966 Planarity : 0.004 0.045 2061 Dihedral : 6.414 86.909 1742 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1612 helix: 0.20 (0.18), residues: 850 sheet: -0.23 (0.39), residues: 187 loop : -0.46 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.005 0.001 TYR D 284 PHE 0.014 0.001 PHE B 353 TRP 0.009 0.001 TRP C 465 HIS 0.005 0.002 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (11633) covalent geometry : angle 0.51528 / 0.27 (15945) hydrogen bonds : bond 0.02882 / 1.93 ( 484) hydrogen bonds : angle 4.06823 / 2.86 ( 1398) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8624 (mp0) cc_final: 0.8375 (pm20) REVERT: A 229 MET cc_start: 0.6100 (pmm) cc_final: 0.5708 (ppp) REVERT: B 198 MET cc_start: 0.8949 (mpp) cc_final: 0.8595 (mpp) REVERT: B 380 LYS cc_start: 0.8396 (ptmt) cc_final: 0.8028 (ptmt) REVERT: B 411 ASN cc_start: 0.9178 (m-40) cc_final: 0.8970 (m-40) REVERT: B 416 TYR cc_start: 0.8355 (m-10) cc_final: 0.8068 (t80) REVERT: C 198 MET cc_start: 0.8681 (mtm) cc_final: 0.8411 (mtm) REVERT: C 207 GLU cc_start: 0.8317 (pt0) cc_final: 0.7460 (pp20) REVERT: C 254 PHE cc_start: 0.8363 (t80) cc_final: 0.7876 (t80) REVERT: C 371 ILE cc_start: 0.9402 (mt) cc_final: 0.8836 (tp) REVERT: D 203 GLN cc_start: 0.9424 (tt0) cc_final: 0.8795 (pp30) REVERT: D 207 GLU cc_start: 0.8089 (pt0) cc_final: 0.7718 (pt0) REVERT: D 293 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7187 (mm110) REVERT: D 372 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7708 (mp0) REVERT: D 375 MET cc_start: 0.9093 (mmm) cc_final: 0.7983 (tpt) REVERT: D 383 GLU cc_start: 0.9363 (pt0) cc_final: 0.9137 (pm20) REVERT: E 203 GLN cc_start: 0.8798 (tt0) cc_final: 0.8520 (tp-100) REVERT: E 207 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7057 (pt0) REVERT: E 219 PHE cc_start: 0.9175 (m-80) cc_final: 0.8819 (m-80) REVERT: E 336 LEU cc_start: 0.9287 (tp) cc_final: 0.9058 (tt) REVERT: E 372 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8541 (tp30) REVERT: E 375 MET cc_start: 0.9063 (tpp) cc_final: 0.8591 (tpp) REVERT: F 229 MET cc_start: 0.8524 (pmm) cc_final: 0.8167 (pmm) REVERT: F 363 ASP cc_start: 0.9379 (m-30) cc_final: 0.8742 (p0) REVERT: F 430 MET cc_start: 0.3522 (mmt) cc_final: 0.3194 (mmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0893 time to fit residues: 21.9272 Evaluate side-chains 125 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046037 restraints weight = 87400.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047107 restraints weight = 59522.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047914 restraints weight = 44319.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048469 restraints weight = 35228.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048802 restraints weight = 29752.066| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11634 Z= 0.149 Angle : 0.564 12.351 15945 Z= 0.296 Chirality : 0.040 0.161 1966 Planarity : 0.004 0.045 2061 Dihedral : 6.420 87.174 1742 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1612 helix: 0.16 (0.18), residues: 854 sheet: -0.33 (0.38), residues: 192 loop : -0.44 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 352 TYR 0.009 0.001 TYR B 386 PHE 0.016 0.001 PHE F 290 TRP 0.028 0.002 TRP A 465 HIS 0.005 0.002 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11633) covalent geometry : angle 0.56436 / 0.30 (15945) hydrogen bonds : bond 0.03119 / 2.09 ( 484) hydrogen bonds : angle 4.38448 / 3.09 ( 1398) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6341 (pmm) cc_final: 0.5970 (ppp) REVERT: B 198 MET cc_start: 0.9000 (mpp) cc_final: 0.8647 (mpp) REVERT: B 380 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8033 (ptmt) REVERT: B 411 ASN cc_start: 0.9203 (m-40) cc_final: 0.8866 (m110) REVERT: C 198 MET cc_start: 0.8776 (mtm) cc_final: 0.8504 (mtm) REVERT: C 207 GLU cc_start: 0.7944 (pt0) cc_final: 0.7091 (pp20) REVERT: C 254 PHE cc_start: 0.8479 (t80) cc_final: 0.7996 (t80) REVERT: C 371 ILE cc_start: 0.9391 (mt) cc_final: 0.8844 (tp) REVERT: C 400 ASP cc_start: 0.8796 (m-30) cc_final: 0.8582 (t70) REVERT: D 203 GLN cc_start: 0.9323 (tt0) cc_final: 0.8831 (pp30) REVERT: D 207 GLU cc_start: 0.8203 (pt0) cc_final: 0.7977 (pt0) REVERT: D 293 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7507 (mm110) REVERT: D 372 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7918 (mp0) REVERT: D 375 MET cc_start: 0.8962 (mmm) cc_final: 0.7963 (tpt) REVERT: D 383 GLU cc_start: 0.9370 (pt0) cc_final: 0.9138 (pm20) REVERT: E 203 GLN cc_start: 0.8777 (tt0) cc_final: 0.8542 (tp-100) REVERT: E 207 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7196 (pt0) REVERT: E 317 PHE cc_start: 0.9213 (t80) cc_final: 0.8900 (t80) REVERT: E 336 LEU cc_start: 0.9376 (tp) cc_final: 0.9162 (tt) REVERT: E 372 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8559 (tp30) REVERT: E 375 MET cc_start: 0.9088 (tpp) cc_final: 0.8585 (tpp) REVERT: E 414 ARG cc_start: 0.9252 (mtp180) cc_final: 0.8960 (mtp180) REVERT: F 229 MET cc_start: 0.8587 (pmm) cc_final: 0.8250 (pmm) REVERT: F 363 ASP cc_start: 0.9368 (m-30) cc_final: 0.8702 (p0) REVERT: F 430 MET cc_start: 0.4067 (mmt) cc_final: 0.3753 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0875 time to fit residues: 20.3394 Evaluate side-chains 122 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 0.0030 chunk 49 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 206 HIS F 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.044549 restraints weight = 91278.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045611 restraints weight = 60407.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046327 restraints weight = 44105.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046940 restraints weight = 35054.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047360 restraints weight = 29331.603| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11634 Z= 0.172 Angle : 0.592 12.381 15945 Z= 0.313 Chirality : 0.041 0.174 1966 Planarity : 0.004 0.047 2061 Dihedral : 6.563 86.733 1742 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1612 helix: 0.13 (0.19), residues: 857 sheet: -0.36 (0.38), residues: 192 loop : -0.52 (0.29), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 367 TYR 0.010 0.001 TYR A 386 PHE 0.015 0.002 PHE D 278 TRP 0.017 0.002 TRP A 226 HIS 0.010 0.003 HIS F 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (11633) covalent geometry : angle 0.59191 / 0.31 (15945) hydrogen bonds : bond 0.03295 / 2.22 ( 484) hydrogen bonds : angle 4.55727 / 3.22 ( 1398) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.384 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: A 229 MET cc_start: 0.6519 (pmm) cc_final: 0.6099 (ppp) REVERT: B 198 MET cc_start: 0.8925 (mpp) cc_final: 0.8574 (mpp) REVERT: B 380 LYS cc_start: 0.8434 (ptmt) cc_final: 0.8070 (ptmt) REVERT: B 411 ASN cc_start: 0.9193 (m-40) cc_final: 0.8863 (m110) REVERT: C 198 MET cc_start: 0.8829 (mtm) cc_final: 0.8564 (mtm) REVERT: C 254 PHE cc_start: 0.8412 (t80) cc_final: 0.7966 (t80) REVERT: C 371 ILE cc_start: 0.9416 (mt) cc_final: 0.8846 (tp) REVERT: D 203 GLN cc_start: 0.9367 (tt0) cc_final: 0.8873 (pp30) REVERT: D 207 GLU cc_start: 0.8229 (pt0) cc_final: 0.7863 (pt0) REVERT: D 293 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7626 (mm110) REVERT: D 372 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7893 (mp0) REVERT: D 375 MET cc_start: 0.8945 (mmm) cc_final: 0.8031 (tpt) REVERT: D 383 GLU cc_start: 0.9316 (pt0) cc_final: 0.9086 (pm20) REVERT: E 203 GLN cc_start: 0.8725 (tt0) cc_final: 0.8523 (tp-100) REVERT: E 207 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7199 (pt0) REVERT: E 336 LEU cc_start: 0.9340 (tp) cc_final: 0.9103 (tt) REVERT: E 375 MET cc_start: 0.8873 (tpp) cc_final: 0.8533 (tpp) REVERT: E 411 ASN cc_start: 0.9287 (t0) cc_final: 0.8840 (t0) REVERT: F 203 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8705 (mm-40) REVERT: F 229 MET cc_start: 0.8498 (pmm) cc_final: 0.8121 (pmm) REVERT: F 363 ASP cc_start: 0.9368 (m-30) cc_final: 0.8668 (p0) REVERT: F 430 MET cc_start: 0.3743 (mmt) cc_final: 0.2792 (mtt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0827 time to fit residues: 18.7664 Evaluate side-chains 117 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** 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 = 0.3220 r_free = 0.3220 target = 0.055795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043896 restraints weight = 89442.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044943 restraints weight = 59450.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045742 restraints weight = 43911.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046311 restraints weight = 34810.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046654 restraints weight = 29175.407| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11634 Z= 0.175 Angle : 0.611 13.694 15945 Z= 0.321 Chirality : 0.041 0.158 1966 Planarity : 0.004 0.045 2061 Dihedral : 6.609 85.357 1742 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1612 helix: 0.05 (0.19), residues: 854 sheet: -0.60 (0.36), residues: 202 loop : -0.45 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 223 TYR 0.018 0.001 TYR E 284 PHE 0.018 0.002 PHE F 317 TRP 0.019 0.002 TRP A 226 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (11633) covalent geometry : angle 0.61060 / 0.32 (15945) hydrogen bonds : bond 0.03451 / 2.32 ( 484) hydrogen bonds : angle 4.63865 / 3.31 ( 1398) Misc. bond : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6676 (pmm) cc_final: 0.6374 (ppp) REVERT: B 198 MET cc_start: 0.8851 (mpp) cc_final: 0.8571 (mpp) REVERT: B 375 MET cc_start: 0.8771 (tpt) cc_final: 0.7677 (tpt) REVERT: B 411 ASN cc_start: 0.9180 (m-40) cc_final: 0.8861 (m110) REVERT: C 198 MET cc_start: 0.8847 (mtm) cc_final: 0.8580 (mtm) REVERT: C 254 PHE cc_start: 0.8373 (t80) cc_final: 0.7939 (t80) REVERT: C 376 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8452 (mm-30) REVERT: D 203 GLN cc_start: 0.9300 (tt0) cc_final: 0.8620 (tm-30) REVERT: D 293 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7781 (mm110) REVERT: D 372 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8101 (mp0) REVERT: D 375 MET cc_start: 0.8960 (mmm) cc_final: 0.8106 (tpt) REVERT: E 203 GLN cc_start: 0.8823 (tt0) cc_final: 0.8485 (tp-100) REVERT: E 207 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7252 (pt0) REVERT: E 336 LEU cc_start: 0.9349 (tp) cc_final: 0.9107 (tt) REVERT: E 375 MET cc_start: 0.9049 (tpp) cc_final: 0.8509 (tpp) REVERT: E 411 ASN cc_start: 0.9364 (t0) cc_final: 0.8878 (t0) REVERT: F 229 MET cc_start: 0.8504 (pmm) cc_final: 0.8139 (pmm) REVERT: F 430 MET cc_start: 0.3779 (mmt) cc_final: 0.3026 (mtt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0852 time to fit residues: 18.9797 Evaluate side-chains 115 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 206 HIS F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044727 restraints weight = 89534.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045813 restraints weight = 58180.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046618 restraints weight = 42065.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047173 restraints weight = 32913.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047606 restraints weight = 27392.224| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11634 Z= 0.117 Angle : 0.570 13.242 15945 Z= 0.294 Chirality : 0.040 0.159 1966 Planarity : 0.004 0.040 2061 Dihedral : 6.454 83.214 1742 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1612 helix: 0.24 (0.19), residues: 854 sheet: -0.21 (0.37), residues: 198 loop : -0.42 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.009 0.001 TYR F 284 PHE 0.012 0.001 PHE A 219 TRP 0.016 0.002 TRP C 465 HIS 0.009 0.003 HIS F 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11633) covalent geometry : angle 0.57020 / 0.29 (15945) hydrogen bonds : bond 0.03120 / 2.10 ( 484) hydrogen bonds : angle 4.26963 / 3.03 ( 1398) Misc. bond : bond 0.00006 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.91 seconds wall clock time: 34 minutes 32.83 seconds (2072.83 seconds total)