Starting phenix.real_space_refine on Tue Nov 18 06:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_8794.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_8794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_8794.map" model { file = "/net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_8794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wc0_8794/11_2025/5wc0_8794.cif" } 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-2.0-5881/lib/python3.9/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: 3.21, per 1000 atoms: 0.28 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: 1.10 Conformation dependent library (CDL) restraints added in 537.8 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: 0.42 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: 1.49 Time building geometry restraints manager: 1.43 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 - 17.83: 6744 17.83 - 35.65: 229 35.65 - 53.48: 50 53.48 - 71.30: 14 71.30 - 89.13: 9 Dihedral angle restraints: 7046 sinusoidal: 2242 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 7043 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: 2.160 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 11.481 89.128 3894 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 covalent geometry : bond 0.00566 (11633) covalent geometry : angle 1.06244 (15945) hydrogen bonds : bond 0.17515 ( 484) hydrogen bonds : angle 9.70112 ( 1398) Misc. bond : bond 0.88791 ( 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 : 0.363 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: 0.8966 (t0) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1135 time to fit residues: 37.1481 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 : 0.351 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 440 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048897 restraints weight = 87693.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.049938 restraints weight = 60343.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050725 restraints weight = 45263.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051346 restraints weight = 36303.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051732 restraints weight = 30507.298| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11634 Z= 0.148 Angle : 0.598 6.305 15945 Z= 0.326 Chirality : 0.043 0.217 1966 Planarity : 0.005 0.057 2061 Dihedral : 12.866 89.627 1928 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -3.02 (0.19), residues: 1612 helix: -1.90 (0.15), residues: 825 sheet: -2.31 (0.33), residues: 185 loop : -1.74 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 352 TYR 0.014 0.001 TYR E 386 PHE 0.016 0.001 PHE F 317 TRP 0.028 0.002 TRP A 465 HIS 0.005 0.002 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00313 (11633) covalent geometry : angle 0.59839 (15945) hydrogen bonds : bond 0.04384 ( 484) hydrogen bonds : angle 5.47027 ( 1398) Misc. bond : bond 0.00641 ( 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 : 0.377 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: A 229 MET cc_start: 0.6844 (pmm) cc_final: 0.6599 (pmm) REVERT: A 372 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8889 (mm-30) REVERT: A 375 MET cc_start: 0.8637 (tpt) cc_final: 0.8336 (tpp) REVERT: A 410 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 198 MET cc_start: 0.9019 (mpp) cc_final: 0.8781 (mpp) REVERT: B 239 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8831 (mttp) REVERT: C 207 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6866 (mt-10) REVERT: C 239 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8391 (mtmt) REVERT: C 371 ILE cc_start: 0.9370 (mt) cc_final: 0.8600 (tt) REVERT: C 400 ASP cc_start: 0.8747 (m-30) cc_final: 0.8491 (t70) REVERT: D 203 GLN cc_start: 0.9357 (tt0) cc_final: 0.8324 (tm-30) REVERT: D 207 GLU cc_start: 0.8044 (pt0) cc_final: 0.6439 (pt0) REVERT: D 293 GLN cc_start: 0.7315 (mm-40) cc_final: 0.7092 (mm110) REVERT: D 372 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 375 MET cc_start: 0.8636 (mmm) cc_final: 0.8084 (tpt) REVERT: E 219 PHE cc_start: 0.9136 (m-80) cc_final: 0.8892 (m-80) REVERT: E 336 LEU cc_start: 0.9462 (tp) cc_final: 0.9177 (tt) REVERT: E 407 THR cc_start: 0.9612 (m) cc_final: 0.9150 (p) REVERT: E 411 ASN cc_start: 0.9152 (t0) cc_final: 0.8811 (m-40) REVERT: E 414 ARG cc_start: 0.9025 (mtp180) cc_final: 0.8814 (mtm110) REVERT: F 206 HIS cc_start: 0.8855 (t-90) cc_final: 0.8525 (t-170) REVERT: F 207 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8104 (mt-10) REVERT: F 229 MET cc_start: 0.8541 (pmm) cc_final: 0.8294 (pmm) REVERT: F 244 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8213 (tpt170) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1093 time to fit residues: 28.2683 Evaluate side-chains 130 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 7.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048202 restraints weight = 86555.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049321 restraints weight = 59036.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050154 restraints weight = 43840.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050708 restraints weight = 34872.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.051207 restraints weight = 29443.867| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3470 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= 0.124 Angle : 0.537 7.144 15945 Z= 0.291 Chirality : 0.041 0.160 1966 Planarity : 0.005 0.051 2061 Dihedral : 11.906 88.767 1928 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.21 % Allowed : 1.81 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.21), residues: 1612 helix: -0.91 (0.17), residues: 816 sheet: -1.70 (0.34), residues: 185 loop : -1.13 (0.28), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 392 TYR 0.011 0.001 TYR C 386 PHE 0.012 0.001 PHE D 278 TRP 0.009 0.001 TRP E 465 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00258 (11633) covalent geometry : angle 0.53669 (15945) hydrogen bonds : bond 0.03754 ( 484) hydrogen bonds : angle 4.72341 ( 1398) Misc. bond : bond 0.00080 ( 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 186 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.434 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: 0.9174 (mt-10) cc_final: 0.8845 (mm-30) REVERT: B 198 MET cc_start: 0.8864 (mpp) cc_final: 0.8598 (mpp) REVERT: B 239 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8915 (mttp) REVERT: B 375 MET cc_start: 0.8941 (mmm) cc_final: 0.7678 (tpt) REVERT: C 239 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8566 (mtmt) REVERT: C 336 LEU cc_start: 0.9446 (tt) cc_final: 0.9190 (mt) REVERT: C 371 ILE cc_start: 0.9371 (mt) cc_final: 0.8982 (mm) REVERT: D 203 GLN cc_start: 0.9466 (tt0) cc_final: 0.8312 (tm-30) REVERT: D 207 GLU cc_start: 0.8131 (pt0) cc_final: 0.6309 (pt0) REVERT: D 293 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7234 (mm110) REVERT: D 372 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 375 MET cc_start: 0.8718 (mmm) cc_final: 0.7999 (tpt) REVERT: E 193 ASP cc_start: 0.8960 (m-30) cc_final: 0.8663 (t0) REVERT: E 219 PHE cc_start: 0.9093 (m-80) cc_final: 0.8784 (m-80) REVERT: E 336 LEU cc_start: 0.9389 (tp) cc_final: 0.9034 (tt) REVERT: E 407 THR cc_start: 0.9611 (m) cc_final: 0.9274 (p) REVERT: F 206 HIS cc_start: 0.8947 (t-90) cc_final: 0.8629 (t-170) REVERT: F 229 MET cc_start: 0.8555 (pmm) cc_final: 0.8214 (pmm) REVERT: F 288 ILE cc_start: 0.9352 (mm) cc_final: 0.9146 (mm) REVERT: F 375 MET cc_start: 0.8453 (mmp) cc_final: 0.8242 (mmm) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.1034 time to fit residues: 27.5957 Evaluate side-chains 129 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN 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 = 0.3309 r_free = 0.3309 target = 0.059169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047134 restraints weight = 89319.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048240 restraints weight = 60402.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049084 restraints weight = 44637.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049614 restraints weight = 35387.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050103 restraints weight = 29829.959| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3978 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= 0.148 Angle : 0.553 9.239 15945 Z= 0.297 Chirality : 0.041 0.131 1966 Planarity : 0.004 0.051 2061 Dihedral : 11.525 89.062 1928 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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: -1.20 (0.21), residues: 1612 helix: -0.48 (0.18), residues: 827 sheet: -1.16 (0.36), residues: 185 loop : -0.88 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 223 TYR 0.034 0.002 TYR F 284 PHE 0.013 0.001 PHE D 278 TRP 0.009 0.001 TRP B 226 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00319 (11633) covalent geometry : angle 0.55291 (15945) hydrogen bonds : bond 0.03578 ( 484) hydrogen bonds : angle 4.54710 ( 1398) Misc. bond : bond 0.00008 ( 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 170 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.359 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: symmetry clash REVERT: A 372 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8803 (mm-30) REVERT: B 198 MET cc_start: 0.8930 (mpp) cc_final: 0.8660 (mpp) REVERT: B 353 PHE cc_start: 0.8965 (m-80) cc_final: 0.8757 (m-10) REVERT: B 380 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8852 (tttp) REVERT: C 207 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 229 MET cc_start: 0.9183 (ppp) cc_final: 0.8887 (ppp) REVERT: C 254 PHE cc_start: 0.8362 (t80) cc_final: 0.7913 (t80) REVERT: C 371 ILE cc_start: 0.9404 (mt) cc_final: 0.9018 (mm) REVERT: D 203 GLN cc_start: 0.9417 (tt0) cc_final: 0.8834 (pp30) REVERT: D 207 GLU cc_start: 0.8060 (pt0) cc_final: 0.7787 (pt0) REVERT: D 293 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7297 (mm110) REVERT: D 372 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 375 MET cc_start: 0.8985 (mmm) cc_final: 0.8148 (tpt) REVERT: E 219 PHE cc_start: 0.9113 (m-80) cc_final: 0.8782 (m-80) REVERT: E 336 LEU cc_start: 0.9355 (tp) cc_final: 0.9012 (tt) REVERT: E 407 THR cc_start: 0.9416 (m) cc_final: 0.9213 (p) REVERT: E 411 ASN cc_start: 0.8614 (m-40) cc_final: 0.8314 (m-40) REVERT: F 203 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8706 (mm-40) REVERT: F 207 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8204 (mt-10) REVERT: F 229 MET cc_start: 0.8602 (pmm) cc_final: 0.8250 (pmm) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.0998 time to fit residues: 24.8702 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 : 0.373 ------------------------------------------------------------------------------- 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: 0.8980 chunk 146 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.0270 chunk 131 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 = 0.3316 r_free = 0.3316 target = 0.058961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047225 restraints weight = 88337.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048349 restraints weight = 59960.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049163 restraints weight = 44364.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049788 restraints weight = 35097.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050154 restraints weight = 29250.198| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4417 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= 0.110 Angle : 0.512 9.540 15945 Z= 0.273 Chirality : 0.040 0.137 1966 Planarity : 0.004 0.047 2061 Dihedral : 11.285 88.149 1928 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.11 % Allowed : 0.74 % Favored : 99.15 % 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: -0.65 (0.22), residues: 1612 helix: -0.07 (0.18), residues: 829 sheet: -0.71 (0.38), residues: 185 loop : -0.63 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 406 TYR 0.006 0.001 TYR F 416 PHE 0.009 0.001 PHE D 278 TRP 0.009 0.001 TRP F 465 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00242 (11633) covalent geometry : angle 0.51225 (15945) hydrogen bonds : bond 0.03273 ( 484) hydrogen bonds : angle 4.20906 ( 1398) Misc. bond : bond 0.00014 ( 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 167 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.415 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: A 203 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8299 (pp30) REVERT: A 229 MET cc_start: 0.6341 (pmm) cc_final: 0.5924 (ppp) REVERT: A 372 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8679 (mm-30) REVERT: A 394 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 198 MET cc_start: 0.8875 (mpp) cc_final: 0.8603 (mpp) REVERT: B 380 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8995 (tttp) REVERT: C 198 MET cc_start: 0.8676 (mtm) cc_final: 0.8325 (mtm) REVERT: C 254 PHE cc_start: 0.8306 (t80) cc_final: 0.7887 (t80) REVERT: C 371 ILE cc_start: 0.9413 (mt) cc_final: 0.8837 (tp) REVERT: D 203 GLN cc_start: 0.9315 (tt0) cc_final: 0.8600 (tm-30) REVERT: D 293 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7327 (mm110) REVERT: D 372 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 375 MET cc_start: 0.8958 (mmm) cc_final: 0.7916 (tpt) REVERT: E 203 GLN cc_start: 0.8754 (tt0) cc_final: 0.8503 (tp-100) REVERT: E 207 GLU cc_start: 0.8293 (mt-10) cc_final: 0.6875 (pt0) REVERT: E 219 PHE cc_start: 0.9109 (m-80) cc_final: 0.8773 (m-80) REVERT: E 336 LEU cc_start: 0.9352 (tp) cc_final: 0.8968 (tt) REVERT: F 207 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8077 (mt-10) REVERT: F 229 MET cc_start: 0.8546 (pmm) cc_final: 0.8163 (pmm) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.0971 time to fit residues: 23.6611 Evaluate side-chains 128 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 0.8980 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 117 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3313 r_free = 0.3313 target = 0.059594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047182 restraints weight = 85000.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048320 restraints weight = 57252.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049166 restraints weight = 42272.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049776 restraints weight = 33459.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050126 restraints weight = 28031.755| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11634 Z= 0.104 Angle : 0.499 10.767 15945 Z= 0.264 Chirality : 0.040 0.134 1966 Planarity : 0.004 0.047 2061 Dihedral : 10.945 86.855 1928 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % 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: -0.48 (0.22), residues: 1612 helix: 0.04 (0.18), residues: 850 sheet: -0.50 (0.38), residues: 189 loop : -0.56 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 406 TYR 0.005 0.001 TYR D 284 PHE 0.012 0.001 PHE B 353 TRP 0.009 0.001 TRP C 465 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00227 (11633) covalent geometry : angle 0.49879 (15945) hydrogen bonds : bond 0.03093 ( 484) hydrogen bonds : angle 4.05542 ( 1398) Misc. bond : bond 0.00010 ( 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 165 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.449 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 229 MET cc_start: 0.6137 (pmm) cc_final: 0.5795 (ppp) REVERT: A 372 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8837 (mm-30) REVERT: A 436 GLU cc_start: 0.7504 (mp0) cc_final: 0.7269 (mp0) REVERT: B 198 MET cc_start: 0.8897 (mpp) cc_final: 0.8556 (mpp) REVERT: B 380 LYS cc_start: 0.9254 (mtmm) cc_final: 0.8927 (tttm) REVERT: C 198 MET cc_start: 0.8712 (mtm) cc_final: 0.8286 (mtm) REVERT: C 207 GLU cc_start: 0.8282 (pt0) cc_final: 0.7503 (pp20) REVERT: C 254 PHE cc_start: 0.8323 (t80) cc_final: 0.7860 (t80) REVERT: C 371 ILE cc_start: 0.9402 (mt) cc_final: 0.8839 (tp) REVERT: D 203 GLN cc_start: 0.9425 (tt0) cc_final: 0.8850 (pp30) REVERT: D 207 GLU cc_start: 0.8040 (pt0) cc_final: 0.7786 (pt0) REVERT: D 293 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7120 (mm110) REVERT: D 372 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7875 (mp0) REVERT: D 375 MET cc_start: 0.9027 (mmm) cc_final: 0.7981 (tpt) REVERT: D 394 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8786 (mp0) REVERT: E 203 GLN cc_start: 0.8878 (tt0) cc_final: 0.8501 (tp-100) REVERT: E 207 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7102 (pt0) REVERT: E 219 PHE cc_start: 0.9128 (m-80) cc_final: 0.8751 (m-80) REVERT: E 336 LEU cc_start: 0.9261 (tp) cc_final: 0.9004 (tt) REVERT: F 203 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8677 (mm-40) REVERT: F 229 MET cc_start: 0.8588 (pmm) cc_final: 0.8210 (pmm) REVERT: F 363 ASP cc_start: 0.9367 (m-30) cc_final: 0.8703 (p0) REVERT: F 430 MET cc_start: 0.3832 (mmt) cc_final: 0.3545 (mmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0996 time to fit residues: 24.3312 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 : 0.417 ------------------------------------------------------------------------------- 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: 0.2980 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3297 r_free = 0.3297 target = 0.058233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046677 restraints weight = 87609.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.047776 restraints weight = 59038.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048499 restraints weight = 43469.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049158 restraints weight = 34619.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049527 restraints weight = 28830.113| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11634 Z= 0.126 Angle : 0.522 11.549 15945 Z= 0.275 Chirality : 0.040 0.156 1966 Planarity : 0.004 0.045 2061 Dihedral : 10.860 89.437 1928 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -0.31 (0.22), residues: 1612 helix: 0.12 (0.18), residues: 854 sheet: -0.30 (0.39), residues: 188 loop : -0.44 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.007 0.001 TYR A 386 PHE 0.011 0.001 PHE E 218 TRP 0.009 0.001 TRP C 465 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00277 (11633) covalent geometry : angle 0.52196 (15945) hydrogen bonds : bond 0.03117 ( 484) hydrogen bonds : angle 4.20127 ( 1398) Misc. bond : bond 0.00010 ( 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 158 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.458 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: 0.6286 (pmm) cc_final: 0.5936 (ppp) REVERT: A 372 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8852 (mm-30) REVERT: B 198 MET cc_start: 0.8904 (mpp) cc_final: 0.8535 (mpp) REVERT: B 380 LYS cc_start: 0.9266 (mtmm) cc_final: 0.8927 (tttm) REVERT: B 411 ASN cc_start: 0.9191 (m-40) cc_final: 0.8918 (m-40) REVERT: C 198 MET cc_start: 0.8766 (mtm) cc_final: 0.8316 (mtm) REVERT: C 207 GLU cc_start: 0.7930 (pt0) cc_final: 0.7026 (pp20) REVERT: C 254 PHE cc_start: 0.8346 (t80) cc_final: 0.7901 (t80) REVERT: C 371 ILE cc_start: 0.9407 (mt) cc_final: 0.8872 (tp) REVERT: D 203 GLN cc_start: 0.9369 (tt0) cc_final: 0.8822 (pp30) REVERT: D 207 GLU cc_start: 0.8071 (pt0) cc_final: 0.7797 (pt0) REVERT: D 293 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7222 (mm110) REVERT: D 372 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8123 (mp0) REVERT: D 375 MET cc_start: 0.8963 (mmm) cc_final: 0.8038 (tpt) REVERT: D 394 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8836 (mp0) REVERT: E 203 GLN cc_start: 0.8728 (tt0) cc_final: 0.8342 (tp-100) REVERT: E 207 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7202 (pt0) REVERT: E 219 PHE cc_start: 0.9083 (m-80) cc_final: 0.8692 (m-80) REVERT: E 336 LEU cc_start: 0.9307 (tp) cc_final: 0.9043 (tt) REVERT: E 375 MET cc_start: 0.8861 (mmp) cc_final: 0.8629 (tpp) REVERT: F 203 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8749 (mm-40) REVERT: F 229 MET cc_start: 0.8535 (pmm) cc_final: 0.8138 (pmm) REVERT: F 363 ASP cc_start: 0.9370 (m-30) cc_final: 0.8715 (p0) REVERT: F 430 MET cc_start: 0.3196 (mmt) cc_final: 0.2324 (mtt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0987 time to fit residues: 23.1958 Evaluate side-chains 124 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046608 restraints weight = 90050.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047592 restraints weight = 60664.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048271 restraints weight = 44843.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048845 restraints weight = 35845.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049201 restraints weight = 30285.122| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11634 Z= 0.120 Angle : 0.512 12.261 15945 Z= 0.269 Chirality : 0.040 0.132 1966 Planarity : 0.004 0.044 2061 Dihedral : 10.730 89.197 1928 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % 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: -0.14 (0.22), residues: 1612 helix: 0.24 (0.19), residues: 854 sheet: -0.15 (0.39), residues: 188 loop : -0.34 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.006 0.001 TYR A 386 PHE 0.011 0.001 PHE D 278 TRP 0.011 0.001 TRP A 465 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00261 (11633) covalent geometry : angle 0.51205 (15945) hydrogen bonds : bond 0.02965 ( 484) hydrogen bonds : angle 4.11522 ( 1398) Misc. bond : bond 0.00015 ( 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 155 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.445 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: 0.6249 (pmm) cc_final: 0.5930 (ppp) REVERT: A 372 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8856 (mm-30) REVERT: B 198 MET cc_start: 0.8933 (mpp) cc_final: 0.8583 (mpp) REVERT: B 380 LYS cc_start: 0.9289 (mtmm) cc_final: 0.8950 (tttp) REVERT: B 411 ASN cc_start: 0.9208 (m-40) cc_final: 0.8922 (m-40) REVERT: C 198 MET cc_start: 0.8824 (mtm) cc_final: 0.8398 (mtm) REVERT: C 254 PHE cc_start: 0.8391 (t80) cc_final: 0.7902 (t80) REVERT: C 371 ILE cc_start: 0.9397 (mt) cc_final: 0.8796 (tp) REVERT: C 400 ASP cc_start: 0.8855 (m-30) cc_final: 0.8565 (t70) REVERT: D 203 GLN cc_start: 0.9435 (tt0) cc_final: 0.8905 (pp30) REVERT: D 207 GLU cc_start: 0.8103 (pt0) cc_final: 0.7886 (pt0) REVERT: D 293 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7434 (mm110) REVERT: D 372 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8216 (mp0) REVERT: D 375 MET cc_start: 0.9026 (mmm) cc_final: 0.8037 (tpt) REVERT: E 203 GLN cc_start: 0.8781 (tt0) cc_final: 0.8369 (tp-100) REVERT: E 207 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7176 (pt0) REVERT: E 219 PHE cc_start: 0.9105 (m-80) cc_final: 0.8634 (m-80) REVERT: F 203 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8701 (mm-40) REVERT: F 229 MET cc_start: 0.8537 (pmm) cc_final: 0.8104 (pmm) REVERT: F 363 ASP cc_start: 0.9368 (m-30) cc_final: 0.8705 (p0) REVERT: F 430 MET cc_start: 0.3793 (mmt) cc_final: 0.2825 (mpp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1017 time to fit residues: 23.1098 Evaluate side-chains 120 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 0.0370 chunk 49 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045895 restraints weight = 86734.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047051 restraints weight = 57277.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047929 restraints weight = 41928.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048515 restraints weight = 32794.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048895 restraints weight = 27274.158| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11634 Z= 0.098 Angle : 0.504 13.273 15945 Z= 0.264 Chirality : 0.040 0.124 1966 Planarity : 0.004 0.043 2061 Dihedral : 10.554 89.552 1928 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1612 helix: 0.39 (0.19), residues: 853 sheet: -0.01 (0.39), residues: 188 loop : -0.37 (0.29), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.005 0.001 TYR F 416 PHE 0.008 0.001 PHE D 278 TRP 0.010 0.001 TRP C 465 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00215 (11633) covalent geometry : angle 0.50439 (15945) hydrogen bonds : bond 0.02808 ( 484) hydrogen bonds : angle 3.95507 ( 1398) Misc. bond : bond 0.00005 ( 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 159 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.471 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: A 229 MET cc_start: 0.6293 (pmm) cc_final: 0.5943 (ppp) REVERT: A 372 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8851 (mm-30) REVERT: B 198 MET cc_start: 0.8957 (mpp) cc_final: 0.8572 (mpp) REVERT: B 239 LYS cc_start: 0.9339 (mttm) cc_final: 0.8696 (ptpt) REVERT: B 380 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8990 (tttp) REVERT: B 411 ASN cc_start: 0.9201 (m-40) cc_final: 0.8882 (m-40) REVERT: C 198 MET cc_start: 0.8793 (mtm) cc_final: 0.8364 (mtm) REVERT: C 207 GLU cc_start: 0.6888 (pt0) cc_final: 0.5789 (pp20) REVERT: C 254 PHE cc_start: 0.8337 (t80) cc_final: 0.7861 (t80) REVERT: C 371 ILE cc_start: 0.9382 (mt) cc_final: 0.9113 (mm) REVERT: D 203 GLN cc_start: 0.9365 (tt0) cc_final: 0.8888 (pp30) REVERT: D 207 GLU cc_start: 0.8076 (pt0) cc_final: 0.7710 (pt0) REVERT: D 293 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7587 (mm110) REVERT: D 372 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8205 (mp0) REVERT: D 375 MET cc_start: 0.9037 (mmm) cc_final: 0.7993 (tpt) REVERT: E 203 GLN cc_start: 0.8806 (tt0) cc_final: 0.8389 (tp-100) REVERT: E 207 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7209 (pt0) REVERT: E 411 ASN cc_start: 0.8821 (m-40) cc_final: 0.8478 (m-40) REVERT: F 203 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8678 (mm-40) REVERT: F 207 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8507 (mt-10) REVERT: F 229 MET cc_start: 0.8459 (pmm) cc_final: 0.7969 (pmm) REVERT: F 363 ASP cc_start: 0.9380 (m-30) cc_final: 0.8680 (p0) REVERT: F 430 MET cc_start: 0.3282 (mmt) cc_final: 0.2649 (mtt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0965 time to fit residues: 22.9309 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045223 restraints weight = 90935.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046245 restraints weight = 60002.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046890 restraints weight = 43750.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047500 restraints weight = 35101.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047835 restraints weight = 29427.202| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11634 Z= 0.154 Angle : 0.539 8.536 15945 Z= 0.286 Chirality : 0.040 0.123 1966 Planarity : 0.004 0.041 2061 Dihedral : 10.708 89.777 1928 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -0.12 (0.22), residues: 1612 helix: 0.30 (0.19), residues: 856 sheet: -0.19 (0.39), residues: 189 loop : -0.41 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 367 TYR 0.011 0.001 TYR F 386 PHE 0.019 0.001 PHE E 317 TRP 0.016 0.002 TRP A 226 HIS 0.005 0.002 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00330 (11633) covalent geometry : angle 0.53923 (15945) hydrogen bonds : bond 0.03092 ( 484) hydrogen bonds : angle 4.25823 ( 1398) Misc. bond : bond 0.00003 ( 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 150 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.383 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 229 MET cc_start: 0.6412 (pmm) cc_final: 0.6063 (ppp) REVERT: A 372 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8861 (mm-30) REVERT: A 436 GLU cc_start: 0.7316 (mp0) cc_final: 0.7067 (mp0) REVERT: B 198 MET cc_start: 0.8998 (mpp) cc_final: 0.8625 (mpp) REVERT: B 411 ASN cc_start: 0.9249 (m-40) cc_final: 0.8924 (m-40) REVERT: B 416 TYR cc_start: 0.7913 (t80) cc_final: 0.7710 (t80) REVERT: C 198 MET cc_start: 0.8918 (mtm) cc_final: 0.8520 (mtm) REVERT: C 207 GLU cc_start: 0.6910 (pt0) cc_final: 0.5665 (pp20) REVERT: C 254 PHE cc_start: 0.8505 (t80) cc_final: 0.8005 (t80) REVERT: C 371 ILE cc_start: 0.9384 (mt) cc_final: 0.9115 (mm) REVERT: C 400 ASP cc_start: 0.8779 (m-30) cc_final: 0.8562 (t0) REVERT: D 203 GLN cc_start: 0.9402 (tt0) cc_final: 0.8923 (pp30) REVERT: D 207 GLU cc_start: 0.8258 (pt0) cc_final: 0.7911 (pt0) REVERT: D 293 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7907 (mm110) REVERT: D 372 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8259 (mp0) REVERT: D 375 MET cc_start: 0.9036 (mmm) cc_final: 0.8078 (tpt) REVERT: E 203 GLN cc_start: 0.8814 (tt0) cc_final: 0.8408 (tp-100) REVERT: E 207 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7317 (pt0) REVERT: E 229 MET cc_start: 0.9323 (ppp) cc_final: 0.9099 (ppp) REVERT: F 203 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8666 (mm-40) REVERT: F 229 MET cc_start: 0.8816 (pmm) cc_final: 0.8348 (pmm) REVERT: F 363 ASP cc_start: 0.9362 (m-30) cc_final: 0.8700 (p0) REVERT: F 430 MET cc_start: 0.3883 (mmt) cc_final: 0.3382 (mtt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1007 time to fit residues: 22.5967 Evaluate side-chains 120 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 89 optimal weight: 0.0030 chunk 149 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3278 r_free = 0.3278 target = 0.057707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045536 restraints weight = 89141.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046669 restraints weight = 58708.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047497 restraints weight = 42982.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048053 restraints weight = 33909.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048499 restraints weight = 28437.637| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11634 Z= 0.105 Angle : 0.529 12.721 15945 Z= 0.274 Chirality : 0.040 0.123 1966 Planarity : 0.004 0.043 2061 Dihedral : 10.487 89.723 1928 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % 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: 0.07 (0.22), residues: 1612 helix: 0.47 (0.19), residues: 855 sheet: 0.06 (0.38), residues: 194 loop : -0.41 (0.29), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.007 0.001 TYR C 386 PHE 0.020 0.001 PHE E 317 TRP 0.013 0.001 TRP C 465 HIS 0.008 0.002 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00234 (11633) covalent geometry : angle 0.52948 (15945) hydrogen bonds : bond 0.02851 ( 484) hydrogen bonds : angle 4.02418 ( 1398) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2085.48 seconds wall clock time: 36 minutes 33.82 seconds (2193.82 seconds total)